Hexes vs squares: seems to be a clear improvement, but if they really did want to simulate a planet it would involve a 3D globe map that was widest at the equator. Would take some working out though.
1UPT vs stacks: never understood why the solution to stacking was to go to the opposite extreme of 1UPT. What about limiting it to a number, with buffs for policies/generals/techs? (e.g. 1UPT at the start of the game, then increasing for techs like Military Tradition, policies like Honour, or just for the presence of a general? or even just reducing combat strength for 'overcrowding', simulating disorganisation?)
Mostly, it makes no sense for me to impose a tactical limitation on what is a global strategic map. (This is more Civ4 vs Civ5 though.)
Tech: SMAC/X actually made more sense to me in the inability to choose your techs; directed research always seemed somewhat odd for ancient civilisations. Obviously, though, making it not decided by the players certainly removes an interesting and important decision.