Opinions and taste are subjective, but here is mine: As good as GCII--ToA is (and it is very, very good), it still can't hold a candle to CivIV. YMMV depending on your tastes. First, I invariably play a turtle/development oriented strategy in TBS games. This is just way more interesting in CivIV since you have a whole lot more development tools at hand. Not only is the entire workers/city resources concept absent from GCII, but the number of city (or planet) developments is limited by PQ. That is a very viable gameplay concept to enforce choices, but to a development oriented player, it is just way less fun than CivIV. Second, the CivIV UI is just much better. Plus CivIV is a much more transparent game. Documentation (by which I mean both manuals and ingame info such as rollovers) has always been Stardock's most obvious weakness. Through the Civilopedia (a feature GCII has always badly needed) and rollovers, information on just about everything is at your fingertips in CivIV. You can calculate, to a couple of decimal places, exactly what the effect of building a city improvement will be. You can't do that in GCII (or at least I have never been able to in several years of trying). This lack of transparancy in GCII has always been my biggest frustration with the game.
I also admit that designing units, which most consider a major strength of GCII, is actually a negative for me. Although I thrive on micromanagement (governors and automated workers are a heresy to me) this concept just leaves me cold and represents unwanted work. I largely felt the same way about unit design when Firaxis used it in the classic Alpha Centauri. (I recognize I was in the minority in both games.) Finally, and this is getting even more subjective, I find GCII (and space 4x games generally) to be a bit abstract. Stardock has done a great job with GCII's graphics, but they are less involving to me than the real world geography of Civ. (Which is a bit ironic since I have been a SF fan for decades.) Nor does building bigger starships provide me with the same satisfaction of moving my primitive civ through the bronze age, the Renaissance, and the Space Age.