From what I've heard on these forums, Kobracan, the minor races will still be present. In fact, it sounds like the development team *might* be planning a few expansions to diplomatic options with said minor races, thus allowing more options of dealing with them rather than trade, bullying, or outright conquest. Granted, I'm not certain, but it's nice to think about!
Also, I was fond of the "racial enmity" present in MOO3, and count it one of the few factors that I actually liked in the game, as it was well-documented in background story and added a distinct identity to the broad racial categories (insectile, saurian, et al.) This sort of "historic antagonism" or even "protagonism," if combined with the alignment options from GC1, could prove a wonderful, rich addition to diplomatic relations in the game. (Let's just hope that it wouldn't prove too big a hassle for the devs -- they've got alot on their plates already!)