I will copy-paste a lot from another topic by Sulla with some good points.
1. Useless messages.
Germany denounces you! Babylon likes you! Russia feels thretened by you! City State X likes Player Y. And miriad other chaff messages that you could not turn off.
Agreed - while it's important to know about denouncements, you've just had the character tell you so...
2. Diplomatic AI.
The long decline of Diplomatic AI started with SMAC. In CivV diplomacy could be easily ignored even on highest difficulties without significant harm to the player. All you have to do is to make some trade deal so caravans will make you some money but otherwise entire aspect of diplomacy could be ignored. AI stupidity in dealing with the player only added to the injury.
I've always disagreed with this, but diplomacy was at its best in Civ V in G&K. BNW added core mechanics that either ignore it (such as caravans and great work swapping), or follow the Civ IV path of giving you blanket positive modifiers for doing what you were going to do anyway (such as adopt an ideology), so that it's too easy to manipulate the AI's relations with you without ever opening the diplomacy screen. The blanket effect these modifiers have on all AIs also dampens the impression earlier versions of Civ V gave of presenting different AI personalities - they're still there, but understated, and don't really amount to much more than how warlike they are and how likely to backstab you.
I still find lux/gold trading and research agreements valuable commodities (though, ironically, I think lux/gold trading should be incorporated into the new trade system rather than diplomacy), but diplomacy has indeed gone back to being the passive exercise of previous Civ games (SMAC was an exception rather than the pinnacle - from memory I think diplomacy was weak in Civs 1 and 2 as well as the subsequent releases).
4. Cities
Even the weakest settlement right after building could beat entire armies of units. While with CivIV one of the main complains were doomstacks, CivV turned sieges and capturing cities into even more horrible and tedious routine. Not to say AI could lose whole army even if it has 10 times more troops than you.
That's mainly an AI rather than a design issue, but one of Civ V's core issues is that the design throughout is not very AI-friendly. The city strength mechanic should probably stay in place of garrisons for defence, but I'd encourage a system where you need defensive upgrades in order to allow the city to shoot, and its offensive ability (and perhaps range - archers on walls shouldn't fire as far as cannon produced from an arsenal) scales with the level of upgrades rather than the city size. That way the city strength stat would be purely defensive, like the melee combat strength stat of an archer.
5. Godawful UI.
CivIV - you could issue build order by ctrl+several clicks...from main map. CivV - to even enter the queue menu, you have to enter city screen, select queque and then click select what you want to build. Even in SMAC it took two clicks to set a proper queue. CivV failed to even recreate that. Not to say that to see how much turns left for workers to finish their tasks you have to hover our mouse for 5 seconds.
6. Awful Diplomacy UI.
It's possible to queue in Civ V?
Yes, that is how bad the UI is. And for goodness sake fix Fortify so that one of the game's most common actions is not hidden in a unit's submenu.
The diplo web needs to return as well - it's not too hard to modify it to incorporate city-states (just add a CS icon of the appropriate colour and type to the side of the leader it's allied with).
7. Meaningless Diplo screen transitions.
Occasionally AI leaders will pop up in diplomacy simply to insult your civilization in some way. To complement you, to say something else that shifts you to diplomatic screen just to look at one like of text that carries no practical information.
I think there should be an option to turn this off, rather than removing it altogether - in moderation it does add character (but the AI is currently inclined to do it rather too often, and there isn't enough variation in the lines it uses to warrant that). It does serve some purpose, as a warning of deterioration or improvement in relations.
Global happiness was supposed to encourage small empires of large, vertical cities. Instead it does exactly the opposite, pushing players into mass spamming of tundra iceball cities. Why not? Once that spot has a colosseum, it's pure profit for your empire. The developers themselves have realized how badly they screwed the pooch on this one, backpedaling in the patch and changing the rules so that a city can't produce more happiness than its own population. If you have colosseum in a size 2 city, now it only produces +2 happiness instead of +4. This changes very little (since it's easy to grow your cities to size 4, and now you can simply cap them there to get the full benefit) while making the mechanic itself much more confusing. Unhappiness is now global, since your population always contributes to unhappiness, but the buildings that fight unhappiness work locally. Also, while a colosseum is limited in how much happiness it can provide by the local city, wonders are unaffected by this rule, as are luxury resources. Uh huh. When you need to start bending the rules like that to cover up mistakes, I'd say it's a sign of shoddy design work. Global happiness is a failed game mechanic.
I agree that global happiness has had its day, but for different reasons. Despite the excessive length of the above section, it oversimplifies the mechanisms Civ games use to limit expansion, because it ignores the time and space dimensions.
The constraints aren't about placing a fixed limit on expansion in terms of number or size of cities (Civ IV maintenance certainly didn't - after a few turns your income stabilised and you could set off again), they're about pacing expansion so that you don't overexpand too early and so build up too many powerful cities from the game's start (while denying territory to everyone else). In Civ IV, you could potentially have infinite numbers of cities eventually - but in practice by the time you had a few up and were waiting to afford the next, all the available territory would have been claimed by someone else.
This is one area where Civ V falls down that's more important than the mechanisms used to constrain expansion: global happiness is a relevant constraint in the early game; post-BNW, financial constraints are a bigger one (since every building has maintenance) - the latter is the reason I'd prefer to remove global happiness since the BNW economic system does its job, and generally better and more 'realistically' (and having negative income in the early game - especially if you have aggressive neighbours - is much more of a penalty than unhappiness or a few percent temporarily added to the tax slider in Civ IV). But there is almost always free territory available because the AI is typically much slower to expand.
A more important issue than global happiness is the other you raised: population=beakers. Expansion isn't just about constraints, it's also about motivation for expansion. Civ V doesn't suffer because it doesn't penalise expansion, it suffers because the reward outweighs the penalty. So you have a system that both encourages expansion and gives you the space to do it in - fiddling with the method used to constrain expansion isn't going to help so long as both of these remain the case.
9. Penalties
Civ5's design suffers from way too many of these penalties, in which the player is actually hurt for doing something good.
This is a curious perspective, since the common complaint - especially from players who prefer Civ IV - is that Civ V lacks meaningful penalties (which I agree with you that it should eschew in favour of trade-offs), where previous Civ games were built around them (such as Civ IV's health system, a novelty which was nothing but penalty, and all prior games' happiness system, the Civ III population cap-without-aqueducts, etc. etc.).
The classic example of this is road maintenance, something new to Civ5 with no previous precedent in the series.
This mischaracterises the maintenance system. Road maintenance is akin to civic or city maintenance in Civ IV, a trade-off where you get the penalty only if you choose to build the improvement/city/select the civic, and in doing so gain the attendant advantages. A strict penalty would be one which simply accumulates or is fixed by itself without providing attendant benefits - such as the Civ 3 cap on population growth without building a structure whose only function is to remove that cap.
In past games, there was never a cost associated with building roads. It was understood that the "cost" of building a road with a settler/worker unit was an opportunity cost, because the unit in question couldn't be building a farm or mine or whatever while it was building a road. In Civ4, for example, building lots of roads early on with workers is a very weak play, because roads only increase unit movement and do not boost tile yields.
This opportunity cost is still there, however in Civ V roads have a persistent bonus - they provide income when connecting to other cities. A one-time opportunity cost that only really applies in the early game, as in Civ IV, is not an appropriate trade-off by itself (and arguably wasn't in Civ IV, where roads connecting other cities provided free and persistent trade income). It's the same reasoning behind buildings - building a granary instead of a lighthouse presents an opportunity cost, but the resulting structure also has a maintenance cost.
But building the necessary road network you need to be safe carries a crippling economic burden in Civ5 - the player is literally getting slammed for good play!
This is a key reason, which you neglected, why the BNW economy is an effective constraint on expansion.
The argument you're making here can of course be made for building maintenance, for the corruption and city maintenance systems in past games, and for past games' happiness and health systems. Expanding cities and growing populations are both examples of good play being 'penalised' by these constraints. Selecting civics other than Despotism etc. is good play in Civ IV, however you're being penalised for doing so by maintenance costs. This is a typical feature of Civ games - the novelty in Civ V is merely in applying the same logic to roads that the prior games apply to most of their systems. And while I agree that it's not an ideal form of game mechanic, it's not a Civ V novelty that should be excised from Beyond Earth, nor indeed is it a feature that wasn't in the original Alpha Centauri.
Upkeep costs for buildings are another giant problem, one which shouldn't be in the game. Civ4 had the right idea in making cities cost money but the buildings inside them be free. Maybe it would be a waste to construct a barracks in a city that never trained any units, however at least you'd only lose out on opportunity cost (you could have spent that time on the barracks building something else).
You have exactly the same opportunity cost in Civ V, and with longer build times (and now, often, more buildings available at any given time) it's more pronounced than in Civ IV, but as above a one-off opportunity cost is rarely sufficient penalty for a long-term benefit. I for one don't miss the struggle to find reasons not to build any and every building I could in every city when short of other things to build in Civ IV.
Those barracks wouldn't *HURT* you just because you weren't using them. Many of the buildings in Civ5 are actually worse than useless, doing virtually nothing while adding to the player's expenses.
They don't add to your expense if you aren't building them; why would you build a 'worse than useless' building? There's also an interaction between this and other game systems - as above it's a key constraint on expansion that underpins the game's economic system, and there are also resource-linked buildings that provide incentives for settling specific resources that provide maintenance-free building options (such as circuses).
It's actually possible to cripple your empire with too much infrastructure in Civ5 if you load up on too many pointless buildings like gardens, stables, and so on.
The whole point is that you shouldn't - it's an incentive to specialise. 'Great People Factories' are the only cities you'll want a garden in, and there's rarely much reason to build a stable outside a military city. These aren't even buildings that have associated National Wonders (not that I'm a fan of the way the National Wonder mechanic works in Civ V - it's nice that they're a bit more distinctive than they were in Civ IV, but 'build X Ys' is a very awkward way to do that).
While this may be realistic in some senses, it's not at all fun and represents somewhat of a trap for newcomers. One of the secrets of high-level play in Civ5 is that you do better by *NOT* constructing most of the buildings in the game, which is surely a failure of design.
You do better by not constructing most of them in most cities. Sorry, but I find it a bewildering argument that it's a failure of design if a game has features newcomers have to learn rather than one in which novice strategies work at the highest levels (as it is Civ V has attracted a lot of criticism for precisely the opposite reason).
Expansion is also rife with further penalties. You want to expand your empire rapidly, because it's the only way to compete with the AI on the higher difficulties and maximize your gold, science, and production. Yet the game simultaneously penalizes you for doing so, by increasing the cost of social policies and making it all but impossible to get additional golden ages.
Yet another reason global happiness is obsolete. Civ V suffers somewhat from having a lot of features added to it that improve elements of the basic game, while at the same time the core elements these replace have not been reworked or removed, resulting in a lot of redundant systems as a result (another, more minor, example is the fact that it has both a trade economy that factors in gold boosts from resources and gold-for-lux trading in diplomacy).
Although Civ4's diplomacy had plenty of its own pitfalls and goofiness, it was actually possible to form lasting friendships with the AI through shared religion, civics, open borders, and the like.
The issue here was much like the issue with ideology and shared religion in Civ V: Most of these are not diplomatic considerations, but are simply things you do anyway that the game rewards you for doing. You're not usually going to decide on civics in Civ IV with the primary motivation that the civ next door hates bureaucrats; the penalty simply isn't steep enough and because diplo modifiers are purely additive, you can overcome it easily with existing bonuses from open borders, years of peace, and trade. You might choose a state religion that way, but since religions don't meaningfully differ from one another in Civ IV this is pretty much cosmetic. Trade just gives you free money so you want it for that more than for free diplo boosts. Open borders is the only one that's actually a diplomatic consideration, and it's one with no downsides.
I much prefer the Civ V model of trying to actively involve the player in directly interacting with other civs, but what we ended up with was a diplomatic system light years ahead of those in prior Civ games combined with an AI largely incapable of using that system - and, as you note, some of the modifiers are ridiculous and in some cases counter-immersive (I particularly loathe "You built Wonders they coveted").
It's essentially impossible to form lasting friendships with the AI civs in Civ5.
You mentioned taking something from Sulla; was this his very old review shortly after release (the comment that 'the latest patch' added transparency suggests it may be). This is not a criticism that's been meaningful since G&K, and it's rather too easy to make lasting friends in BNW (though when ideology hits that will completely screw up the system by forcing you to go to absurd lengths to remain friends with someone who's been a lifelong ally but just happens to have a different ideology). Even in vanilla it was far from "essentially impossible" at least as high as Emperor (the level I played at back then), when I did it routinely.
Compare the same diplomatic situation to Civ5. What can you really do diplomatically with the other AI civilizations? Tech trading was axed entirely from Civ5, removing the single biggest incentive to work together from past games.
You're rather overselling the way the past games handled this. You could tech trade with civs that had pretty much neutral relations with you, and if you traded well to begin with you'd soon be far enough ahead that the other civs had little worth trading, rather confining relevant diplomacy to the early game. The only reason for actual alliance was diplo victory and the UN.
In Civ V, civs don't seem to allocate votes (or agree to vote-trading) based on their relations with you at all, and diplo victory relies less on other civs than it did in G&K. In short, none of the games give you very much incentive to maintain alliances - Civ V forces an artificial situation where you need friendship for research agreements or lump sum gold deals, but while it works fairly well it's not an ideal fix.
Map trading is also gone. You can still trade for Open Borders, but they no longer have any effect on trade routes, and thus have only a minor importance now in the gameplay.
They're very important for spreading cultural pressure and necessary for exploring the map - moreso than they were since map trading is indeed gone.