Help us out. If you find such a game let us know!
I doubt that what you are asking for is important enough to the "average consumer" who will buy these games to get a game writing organization to address it. If it was surely the game would have been written this way.
I think your best hope is to try to support the movement to get the source code for Civ 2, then work on improving the AI for that (or hope someone else does).
Or maybe someone could get some concrete market analysis indicating such a game would sell millions of copies - more than just the flashy graphics or new units.
I held out buying Conquests for a while, because I think Firaxis/Atari could do a lot better making the game better the first time so we could avoid the frequent patching. In the end I gave in because I wanted to share my experience with other players, and it wasn't working too well when they were on C3C and I was on PTW. By waiting at least I avoided all the initial bugs that I knew would be there. Atari should thank civfanatics for my purchase of C3C! I am quite sure I would not have bough it otherwise.
I have probably spent $100 on all 3 discs, but when you consider how many hours I have played this game, the entertainment value was well worth it, patches, weak AI and all. How many hours at the movies or at concerts would you get for $100?
One more thing - you will probably never get a satisfactory answer to the missing file problem. There are no more patches coming out for vanilla Civ 3. So either try to get the thing working again (reinstall or whatever) or deinstall the game and move on to something else. There's not much other choice. Good luck.