Here are a few things:
1) I'm a huge fan of the civics system in this mod, and it's probably the main reason CoM is my favorite way to experience Civ 4. The civics profoundly impact how the game is played and allow for far deeper strategy than what is available in vanilla Civ. The depth of the civics system also goes a long way toward making the game feel realistic: running a slave society should feel very different from running a libertarian socialist utopia, and CoM's civics deliver on that front.
2) There are, in general, too many buildings, and too many of the buildings aren't really buildings. I don't feel the excess of buildings necessarily throws the gameplay balance out of whack, but it doesn't feel as gratifying to build things in CoM because so many buildings (apiaries, wheelwrights, etc.) seem like they're not supposed to provide meaningful bonuses in themselves, even in their appropriate eras. This is a problem a lot of Civilization (i.e. not just Civ 4) total overhaul modpacks suffer, but still.
3) The most recent edition of the mod crashes... a lot. I don't recall the mod crashing this much before. Most crashes seem to occur either when I load a saved game or when I end my first turn after loading a saved game. Notably, the crashes aren't reproducible: if the game crashes and I start it back up and do exactly the same things I did before, it doesn't seem like the game is any more likely to crash than in any other circumstance.
4) All of the AND map generators seem to not generate very many sea-based resources. I know this because I have a habit of regenerating maps until I get a start with a lot of fish etc.. Using the non-AND map generators seems to rectify this, though I don't know if I should be doing this. Is this intentional?