I think they'll accomplish this with the new culture, trade, religion, and tech tree systems. The new culture system will make it harder to hold on to conquered areas, or even areas that you have just neglected culturally, the religion system will allow smaller, but religiously expanding empires to have a huge influence on the larger ones, the new tech tree system will allow smaller nations to catch up to larger ones militarily by sacrificing civil technology, and if you have a small nation with lots of resources it could make you extremely valuable to the nations with more passive AI.
Speaking of the AI... its nice that they're going to have multiple leaders for some nations, with different AI and such. The fact that pretty much everyone had the same AI in Civ3 bothered me. God damn warmongering Ghandi.