Finally, what I've generally found to be the case with most Civ games is that the end game usually isn't as enjoyable as the beginning of the game. This is mainly because there is no more exploration to be done and all of your cities have dozens upon dozens of the same buildings, and the only thing really left to do is go to war or win the game.
Very, very true! Besides what you're saying, it also starts getting tedious and feels like a big grind maintaining all these cities, especially the relatively newer ones you don't really care about that you might have built because they're near a vital resource (oil, uranium, aluminum, whatever). Puppet cities were a great addition to Civ V but you can only currently create them by capturing an enemy city. It would be nice if you could create one yourself that you didn't want to micro-manage. That is, is there a way to either create or turn cities into puppet cities you build yourself? I'm thinking an ideal solution would be a government policy must first be unlocked that "enables de-centralization" and then a custom building built (call it a courthouse) that turns the city into a puppet city. You could, of course, annex it back just like you can do to puppet cities now but it would cost you unhappiness/stability until you got (another) courthouse in. So, every time you toggle back and forth between full city and puppet city the existing courthouse (if one exists) would be destroyed and you have to (re)build a new one before the city changes (back). At some point, especially in the late game, I stop caring about micromanaging, but I don't want to necessarily just build a large queue because as technologies are discovered, the list might change and I don't want to just necessarily set it to build wealth or science so as to avoid managing the city; puppet cities are a good feature, I just wish we could make them and/or toggle back and forth (for a penalty) late in the game.
On a related note, would it be possible to create an "immigrant unit" that costs 1 population to create that when sent to another city (or traded to another civ) can increase its population by 1? I know there's some Civ IV mods that have this ability (though I don't think they penalize the city the immigrant came from like they should). This would be a good feature in the mid-game when you're expanding and you realize some of your frontier locations are better areas to be settled.
Switching ideas, I absolutely think "tech diffusion" should be in the game. At some point, every civ should stumble across the knowledge of technologies that other civs have unlocked. I like the concept of open borders means
higher probability of you both being given technologies the other possesses, so it makes open borders actually mean something besides just passing units through. I also think there should be "espionage" buildings that you can construct that serve no other purpose than to increase your civ's probability for acquiring free techs that other civs possess (ideally the highest probability would be for techs your neighbors posses that you don't and/or civs you have open borders with). Of course, you have to be careful, because they could do the same to you.
In fact, all techs should be unlocked in a somewhat random fashion. That is, make the number of turns it will take to unlock a tech the EXPECTED VALUE (ideally, somewhat normally distributed around this value) and not just fixed. So, if it says combustion is 18 turns, it might really take 12 turns or it might take 24 turns. You just never know either way until 'surprise! your scientists have discovered it!' This kind of randomness will add excitement to the game, especially the late game when things get more predictable (read: boring).
Another tech-related question: will Civ V ever make it possible to research more than one simultaneously? Say, if you construct the "National College" national wonder then you can unlock the ability to research two things at a time, albeit you don't get to throw full science points at both, you still only get as many total science points as you have, but you could at least study two techs at once, say dedicating 2/3 of your science to tech A and 1/3 to tech B. When you couple this with making the unlocking of techs random then it's POSSIBLE you might discover BOTH earlier than you otherwise would (of course it might also happen it takes you longer to discover both). But, since the number of turns isn't a certainty but instead the mean, or expected number, things still work out on average (across civs, across techs/eras, across games)
I also miss the culture diffusion of Civ IV. It made culture really mean more than just unlocking policies and/or shooting for a cultural victory, it made it really "mean" something if that iron (or city) on you and your neighbor's border is swaying back and forth between who it belongs to. In the late game, this was a way to capture cities without having to go to war. In other words, it added a dimension to the game (especially late game) that is lacking in Civ V (currently it's too one dimensional - you have to go military like you're saying, which can become a grind with so many units late in the game)
Lastly, I always prefer keeping things as realistic and historical as possible, but I do think it would would be interesting to see "space aliens" randomly appear in the game as "modern barbarians" beginning in year 2001. They would have flying saucers (air units), encampments located in the sea, and infantry units that can fire lasers and immune to existing military units. The only way to kill their land units would be with a modern drone unit (that requires uranium). Adding these modern alien barbarians would force users (and AI) to consider land, air, AND sea units to ward them off and not have their modern cities taken over. It might also prompt civs to form more defensive pacts to help each other out. As Civ V stands, you almost have no motivation to create navies, but with alien encampments out at sea, you'd have to root them out.
Another easy way to make navies matter again is to not let units cross ocean tiles (coast tiles ok, but not ocean tiles) and go back to Civ IV style of requiring they must go aboard naval transport ships to take them across the ocean. Settlers, etc. should all be moved across the ocean this way.
Maybe make a new town type (analogous to puppet cities) called "colonies" that can ONLY be built in areas that are separated from your capital by ocean tiles that give huge cultural bonuses and make it a REQUIREMENT to win a cultural victory that you posses 3+ colony cities. Besides benefiting the mid-game with huge culture bonus, this would also make the late game more exciting by either a) make your really protect these distant colonies and/or b) make you scramble to seek other civs colonies out and capture them
One more late game idea: bring back random environmental disasters, proportionate to your "number of hammers". Don't call it (local) "health" (like Civ IV), but call it "pollution" and it can randomly strike your precious resource tiles (oil, uranium, aluminum) not only taking out your improvement, but the actual resource. So, you better protect them by adopting government policy that reduces the risk and/or constructing buildings that help reduce the risk.
Well, I know this is a lot to chew on and most of it probably not even doable in a Civ V mod, but basically anything that introduces more a) randomness and b) competing alternatives to choose from would help liven up the late game.
As far as your mod goes, it's THEE mod I play with. And I really like your concepts and very much looking forward to V9! Maybe you'll agree with some of my ideas and work them into V10 someday. I've thought about getting into modding Civ myself, but people like you do such a great job - and I can only imagine how much work you pour into it - I know I probably couldn't come up with something 1/2 as good as you have with Civ NIGHTS!