Thsi point may be down to me not having a full game.
Or possibly the whole post is because you haven't played the whole game?

I was a lot more pessimistic about the game on my first 1-2 playthroughs, but after getting into it, it is overall a very strong game, even if it doesn't have the polish of BTS, which had 4+ years of sheer development put into it. It's a fun Civ game that has quircks that I'm sure will be fixed soon. It's by no means a disappointment, though, and calling it rushed is incorrect. That's not to say there are some bizarre omissions here (the lack of movement trails for units you have traveling multi-turn distances being a glaring one), but there's also a lot of changes that are a vast improvement over CivIV (combat, the notification system).
The thing is, while change is obviously not fundamentally wrong, are the changes and omissions really good? Have the removed options been replaced with anything? Is it better than civ4?
You're likely talking about health and religion here. The concept of the city having a value that has the potential to impact its growth specifically is something I would agree should have continued from CivIV, if only having health instead of both health and happiness. I like empire-wide happiness, it's s good concept, but I think completely stripping city management is not so great: it really devalues city placement. No longer do you have to be concerned about settling near too many jungles or cutting down too many trees (the food/hammer bonus in Civ5 just isn't compelling enough, compared to the 20 hammers anymore, early on).
I know their philosophy was to reduce micromanagement, but with it completely gone cities just aren't special or deserve any attention anymore: it's all big picture, and I personally don't care for that, although sometimes I do like to just put things on autopilot during wartime. The issue here is that adding too much micromanagement because extremely tedious and strips all sense of fun: the game becomes a simulation, not a 4x. I think CivIV was too much of the former and CiV is too much of the later, we need a balance. Adding city health back would be a great way to do this: keep happiness empire wide.
Cottages. What was wrong with them? IMO it was one of the most inventive additions to the game since civ1
I like trading posts better (they don't clear forests or jungles, like cottages do). They also don't work with the gold system: having a town that gives 8 gold is unbalanced: gold is meant to be harder to get in this game. Remember that a town actually gave a large amount of commerce, which was then funneled into research, gold, and culture (and espionage later). Now it's just gold. I'd say culture was much more inventive than cottages: although they did have a nice long-term benefit. Every other improvement has always been immediate, improved later by techs.
religion - again, added a lot of options, a lot of choices, like building temples in cities that wouldn't otherwise need them at the time, to help another city's culture by allowing a cathedral
I'm sure they'll add it in some form in some expansion pack: it's been reborn in the piety social policy tree, which I find very useful (if you're willing to sacrifice the science benefits of rationalism). Sure I'll miss raking in gold from spreading my religion, but I think this is where the role of city-states come in: they added an element for you to micromanage with. They could have added religion, corporations, on top of city-states, but that is a lot of concepts for someone new to the game to pick up. That's why corporations were added later in an expansion: by that point people were familiar with the base game and were able to handle more elements throw in the mix. Is it not possible for you to enjoy the elements that are in the game, without pining for things that aren't there?
not having to connect a resource to the city to be able to use it? Really? I haven't played that much but does it mean that if I build a city 15 hexes away from any settlement with no road and sea access, it will be able to use all of my strategic resources? And if that city has a strat. resource, I can use it on another continent? Thsi point may be down to me not having a full game.
Or how about in CivIV, when you had a resource on a one-tile pennisula that was blocked by a mountain: it happened to me once and it annoyed the hell out of me. It was in my cultural borders and I would never be able to access it, since I couldn't connect it by road to any city. Because roads costs 1GPT now, it would be prohibitively expensive to connect all resources with roads: they did this to remove the road spaghetti that has been so prevalent in the last two civ games I played: it looks ugly and doesn't look very realistic either. If it's in your borders, and you've built the improvement that connects the resource, then it's yours. What's so wrong with that? Maybe it helps if you imagine that roads are actually major roads, like highways, and smaller roads are invisible in the game, but still connect your cities together

.
espionage - I never liked it in civ4, I thought it was a rushed and simplified addition but it was there as an option, as a strategy choice. It needed improving not removing. What is there in civ5 instead? As I said, I do not know civ5 extremely well so maybe I miss something there.
It was a nuisance in CivIV, and it was interesting, but kinda pointless, in CivIII. I don't think they've ever gotten it quite right, and I wouldn't care if it never got implemented again: it usually involves way too much micromanagement. Man this is long...I don't know if I have the stamina to respond to everything
generally, I have a feeling that almost everything was tuned down to have less influence
Yes, individual resources aren't quite as powerful as in CivIV, but there's quite a few more on the map than before: it's not unusual to have 4-5 resources in your cities workable tiles. If that situation occurred in CivIV, you would have a massive, powerhouse city. It seems more balanced now, so that civ's that start in crappier locations (read: the never ending tundra of hell) won't be at a permanent disadvantage. It was never fair to start in the middle of the desert, but now you can actually build farms there now (it's not realistic, but it's a hell of a lot more fun).
science now is down to pop mostly. How can I influence the science output significantly? OK, it may be "realistic" to say you can never FORCE a nation to suddenly become a source of new ideas and technologies, but this is not a real life sim, it is a strategy game, in which all aspects should be controllable, but always at a cost, ie more science = less food/gold/happiness/tanks whatever. Just let me control it even indirectly.
I think you need to play the game more on this point: you can control it nearly as much as before, there's just no more artificial sliders that force you to choose between gold or science (or culture). If you want a city to be more focused on science: build a library there. It's a 50% increase, so is a university. Also, you can direct Great Scientists to build their academy improvement on one of that city's tiles: 5 more beakers there. The sliders were goofy and I don't miss them at all, they were very lazy too (which no one ever seems to mention). Now, when you want to focus on gold, you actually have to put some effort into: build improvements, focus on gold buildings, disband unnecessary units. Before, you could just ratchet down the research slider. Kinda dumb.
corruption - where is it? I haven't investigated this too much, but from what I saw the distance between cities plays no role in the maintenance now. Or in their production effectiveness. If that's true, it is another huge simplification.
I'm actually a bit torn on this one: I hated corruption in CivIII (lost food and production as well), but it was handled well in CivIV. This was an unnecessary simplification, but adding it back in to CivV would require completely rebalancing gold in general, something I doubt they'd be willing to do. They should have never removed it in the first place: cities that are farther away from the capital should be expected to be prone to acts of corruption: its a realistic flavor with interesting gameplay impact. To be fair though, in CivIV it was completely moot once you had state property: the maintenance for number of cities was laughably low. Rolling all this into happiness: pretty extreme.
happiness is now empire wide...
Less micromanagement: there were two city-specific numbers you had to be careful about in CivIV: health and happiness. Like I said above, removing one was OK, so I like empire-wide happiness, but having both disappear doesn't work well (explained above). The only problem I have with empire happiness is that it rolls city happiness, health, AND corruption into one number. Removing corruption is just ridiculous: it doesn't require much micromanagement. You know which cities are far away from the capital: build a courthouse and move on...
social policies - a lot has been said about them. I just like to add that I always thought there should be two things in the game: a civ's social values AND (as a separate thing) political/government choices. The first should not be a subject of player's free decision, rather reflect his general play
Disagree with you: I don't like anything that takes away a player's choice: that's just the wrong way to approach game development. Civ is always about making choices, and having those choices that YOU made impact the world around you. I don't disagree with having social values and government as two separate things: it's an interesting idea that wasn't implemented, but I wouldn't hold it against the developers. Social policies are already quite extensive, with all sorts of choices to make. Having an additional system might be a bit too much for the vanilla release.
One that that has disappointed me has been the level of difficulty: I use to be able to play chieftain with some element of challenge (and having to make tough choices at times). The way empire happiness is set, plus the AI being rather poor at combat (they seem to rarely garrison units in their cites) means I'm going to have to go up 2-3 difficulty settings to get the same experience I had in CivIV. I couldn't imagine gamers who were playing at Immortal in CivIV: maybe the AI (hopefully) ratchets up dramatically at a certain point. They're speedbumps on my path to world domination on chieftain.
Edit: I was waiting for the forum system to tell me to stop typing...apparently there's no character limit here?
