Fascinating, and wonderful to see others are out there who are weird like me, and who will actually attempt to extend Civilization games over extremely long periods. I have a Civ4 game that I've been playing for about 4 straight years now, and admittedly the file has gotten so big that it periodically taxes my system resources to their limits (Unfortunately, Civ4 suffers from poor memory management and is fairly leaky. Especially w/ mods).
The problem with Civ4 is that the AI is so hyper-aggressive that long-term stability is all but impossible, unless I become a dominant superpower and take on the role of "world police," intervening in every war of aggression on the side of the underdog. But after awhile, there's really no fun in that. So I have tried to cultivate a game in which a few superpowers are at least my equals, if not my superiors. Since I'm always going to war to defend whoever's about to get wiped out, unfortunately, I'm switching sides constantly, and diplomacy is basically out of the question. (None of the AI players will even return my calls, so to speak. We've all nuked each other so many times over that we won't even speak to each other now).
The other problem is that the AI fights total wars by default. It will never engage in a limited conflict. No, when it declares war, it won't cease until either it's beaten or it totally annihilates its enemy. It's like a Terminator. It becomes quickly apparent that the Nash Equilibrium in a game of Civ4 is one nation standing, while all others have ceased to exist. The game drives ineluctably toward this conclusion, unless the human player puts aside his own nation's interests in pursuit of global stability and game longevity. (And, ironically, being the sole force for stability renders him a political pariah among all the other nations). It's sort of like trying to play one sport, when all the other players in the game have been programmed to play another.
Sometimes I wish the AI were more sophisticated, and/or that it could be incentivized to prefer economic growth and interests over nonstop warmaking. Or that one possible victory condition in a game of Civilization would be to maximize a global human development index of some kind (i.e., "Global Victory," instead of just one nation's domination of all others by X or Y measure, or else its complete extirpation of all other peoples on the planet). I realize that's not the game that 99.99% of Civ players want to play, but it's refreshing to hear that I'm not the only one.