2. The AI, particularly early in the game, doesn't seem to play to win, it seems to be doing its best to be as irritating as possible. Ive had up to 3 civs march 30 hexes across the map to plant a city so close to my territory that two of them didn't have a clear hex around it. In occasional games, even on lower difficulty levels, for no apparent reason, civs attack you aggressively en mass, with surprising co-ordination with the barbarians, who will hurl themselves to death on your city walls, rather than capture a worker or pillage an AI civ much closer to them. While this does increase the difficulty, I have the difficulty slider for that.
3. Ridiculous trade agreements keep being offered to me, turn after turn. The diplomacy screen is slow, even if you escape out of it. I don't need to keep seeing offers for me to trade all my luxuries and gold, for open borders 20 turns in a row, from 3 civs. How difficult is it for the AI to stop offering stupid one-sided deals?
5. Religious warfare; surely a case of the emperor's new clothes, no one willing to tell Ed how much it sucks. I am not opposed to the idea of a religious victory, but not only does the system not begin to give a respectable representation of religion (not essential I know), but religious combat is just another version of military combat, with all the fun, complexity and interest taken out. The question isn't whether it is enjoyable, but how could anyone think it is enjoyable.
8. The start screen and main menu has features removed even from Civ5. The high scores table, and the ability to change the default create settings are gone, for no other reason than they were too lazy to include them. So you start a game and suddenly realize you forgot to set the speed to quick, so back out; start it up again; crap, I forgot to change it from random civ; start it again; lousy start, restart; start it again, oh crap, speed setting again! Give up!