This is an excellent list! Numbers 2, 3, and 7 on your positive list are very interesting observations about core design elements.
Thanks. I agree with a lot of the criticisms regarding the awkwardness of 1UPT, but I like many of the changes that are linked to it (slowed production is a better fit for the game pace and limits the amount of tedious unit spam required by the older games) - the one I listed is among the more subtle and less-discussed, but it really does give a sense of genuine change over time rather than "my units have bigger stat bonuses now". Air power has been treated differently from other units since Civ III, but aircraft didn't really change the way wars played - I think Civ V is the first game to really nail it.
As for your negative list:
I'm not really sure that your criticism of ideologies is fair. You can think of this as an abstraction of something akin to "regime change".
I'm not opposed to the general idea, but to the extreme impact it has on the late game: everything in the late game is about ideology, and you have very little ability to influence which ideology long-time allies adopt (quite unlike reality, really). So you can find yourself at loggerheads with a formerly dependable ally just because they were the second to reach the Modern era and the AI likes to take an available ideology with free tenets over one that matches its allies'. And while the idea of replicating the Cold War is nice, there isn't actually a way within the game to really simulate Cold War conditions - proxy wars rapidly lead to real wars.
Having ideology affecting all powers equally is necessary as long as the game doesn't really have a way of distinguishing between players performing well and those performing badly in its modifier system, but it's not very satisfactory. During the Cold War, the US simultaneously existed in a state of cold war with the Soviet Union while according Most Favoured Nation trading status to China, and while it was concerned about a 'domino effect' turning India Communist, no one cared about India's choice of government in and of itself, only for the extra influence it would have given their main rivals. No one planned an invasion of Madagascar during its communist era, and so forth.
A civ will only really care about ideological choices of its major rivals - BNW even offers a mechanism to simulate this: just have a diplo modifier based on a civ's cultural influence over other powers (negative if that civ has an opposing ideology, positive if the ideology is shared). In general, ideologically differences will be subservient to all the other factors that make two major powers rivals to begin with.
There's also no post-ideology era; once ideology comes into play, games play basically identically every game, with ideology blocks squaring off and wiping out the weaker powers.
The same applies for changing civics in Civ IV or government types in earlier Civ games. If a society changes its core, fundamental beliefs, then yes you should expect that their relations with other societies will change. I think the only real problem is that your civ's "personality" and none of your earlier development choices influence your ideology.
That definitely is an issue - BE's affinity development offered an interesting model for a future Civ game's ideology system in principle, but was a great disappointment in practice.
I wouldn't mind a system in which your ideology emerged organically from choices earlier in the game, or if those choices would be mechanically enforced by the game. For example, building a trade-based empire and dominating the world economy through trade routes and resource exchanges could perhaps give your civ a bias towards adopting Freedom. Conquering other civs would give you more bias towards Autocracy. These biases could affect the cost of adopting those ideologies (i.e. higher biases make them cheaper to adopt so that you can adopt them earlier and benefit from them longer), or it could affect happiness levels after adopting the ideology, or it could affect the strength of the actual tenets.
All good ideas (though conquering the world biasing you against a democratic, trade-based ideology plays against the real-world history of the British Empire...)
As for random events: those have proven very unpopular from what I've heard. Also, the idea of completely random events is kind of absurd except for maybe weather and natural disasters.
Civ IV implemented random events very poorly, with effects that were often too unbalancing and simply too common, but that shouldn't be taken as a reason to eschew random events altogether. We already have randomness from huts, after all (and I mourn the loss - in both Civ IV and Civ V - of barbarian spawns from villages. Exploration should have its perils). And events need not be fully random, but can be things that your decisions can influence - for instance, following the original Civ board game, volcanoes are only in certain areas and you're only going to be hit with floods along major watercourses like the Nile. There was a good Civ V mod that added a plague and health system, where plague would strike randomly if you didn't maintain good city health.
It was too unbalanced to make for good gameplay, since the health structures weren't things the AI ever prioritised building so your AI rivals invariably got wiped out by plague and/or acted as reservoirs that spread disease to your own cities even with good health management, but it would be a very good basis for a disease system if Civ VI were to incorporate one from the ground up and code the AI accordingly. Other manageable events like civil wars or, indeed, uprisings would be welcome - Total War games have always had ways to simulate this, though not always well (and in the first two Civ games, widespread unhappiness would lead to civil wars).
What I think really needs to be changed in this game is the fact that you can only have 1 of each wonder. If 2 people are building a wonder at the same time and one person gets it 1 or 2 turns sooner the other person gets practically nothing for their efforts.
That's the whole point of Wonders - change that, and you may as well remove them altogether. As another poster mentioned, this is a cornerstone of the series. More importantly from a design standpoint, Civ is a series that has traditionally allowed very little meaningful interaction between players - it's not a game like chess where you get to directly respond to an opponent's moves by countering them with your own, or like Starcraft where you can actively deny the opponent resources. You can manipulate them in ways that help you (such as tech trading), but you can't do very much, aside from occasional espionage missions, to actively set your rivals back. All you can really do is optimise your strategy so that you win the race to the finish, or go to war to finish off rivals dangerously close to victory. Wonders are the one big exception to this, the one tool you have that can actively deny options to an opponent rather than just helping you get ahead faster.
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But I cannot help but feeling that turning Civilization into a more boardagme-like game is akin to taking one videogame RPG like the Witcher back into its pencil and dice roots. It sacrifices a lot (flavour, inmersion, complexity) for a very paltry return (cleaner game design, better multiplayer component), and it has lead to some erroneous game design decisions due to refusing to acknowdegle that different mediums have different strenghts and limitations.
