Keep in mind that part of my goal for changes was to ensure that each era's soundtrack would be totally unique; this naturally will lead to a winnowing of total songcount per era.
As for the songs:
CIV III Modern Middle East is a deceptively complex melody; there are several riffs and rhythms clearly identifiable as being of the Indian subcontinent, and while it's drumbeat places it as firmly Ancient, not Classical, it still seems both too culturally specific and too sophishticated to be of the Stone Age. The Native American tracks don't have this same issue with cultural specificity, since that society stagnated at a Neolithic/Chalcolithic era (late Prehistoric/early Ancient) for the sum of it's existence anyway. With Prehistoric, I like to think primal, animalistic and tribal beats.
Both incarnations of Conquests Fantasy scream Medieval to me, as blatantly as rock music screams modern and techno Transhuman; if you can tell me what you see as "Ancient" or "Classical" in them, maybe I can offer a more objective review. The imagery it calls to me is that of a stone castle surrounded by serfs, where knights ride astrode paved roads and guards with pikes in chainmail armor argue with elaborately clothed merchants.