--When a unit with long-distance move-to orders has its destination blocked, it will shed its orders and request new instructions with no reminder of what its original move-to destination was. Very frustrating later in the game, when you have multiple units moving to multiple spots on the map.
--Trading posts that continue to look like medieval-era bazaars well into the modern era and beyond. Not at all the end of the world, but kind of irksome. (I've heard of trading posts updating to shopping-mall structures, but I've never seen that in my games.)
--Singapore's music. And the fact that I ALWAYS have Singapore in my games.
--Non-spreading forests. I miss CIV's forest growth. Utilitarian value aside, it made the world feel a little more dynamic and alive, less like a static (animated) painting.
--The "narrator's" intonation and articulation of certain tech/wonder/etc. quotes. Doesn't seem quite right in many places. Granted, Leonard Nimoy is a tough act to follow, but still.