1) for me the graohics annoy me. I don't know why, but I can't tell what's going on or where my borders are. Diplomacy also doesn't really make sense, I have never seen a civ that would actually switch religions, and it doesn't make a difference because their cities don't actually change religion if they convert.
2) I thought that there could be a lot of really great features put in this game that were left out. I hate the reiligion system you can't wipe out religions and stuff and the way that religion spreads doesn't make sense. I was hoping that you could make your own religion...not because people might get angry if christian germany attacked a jewish civ in one game, but because it would be really cool to design your own religion that would grow and change, and that way the religions could be different. One could be warlike, one industrious, etc. I guess I was just dissapointed so much was left out. And you can't access the map editor from the main screen! only in a game. Grrrr
3)The game got more streamlined. It got shorter and more like an rts. You could play more games in a shorter amount of time. It kept it's civ characteristics, but it did "rts-ize" itself. Personally I didn't like this. I liked the long drawn out games of civ3. But that's just my opinion.
-I play civ4, but I think it lost some of the "Umph" of civ3. But the civics system is cool, but i wish you had the option of making the game more detailed. So people who didn't want to have a more detailed game they could, but didn't have to if they didn't want to.