One major quitessential "Civ" thing I'm not seeing so far are natural wonders. I did see one fairly unique feature, looked like a large crater (very similar to the Barringer crater in AC) but it appeared to be purely visual and without any bonuses: mousing over the central hex (the mouth of the crater) and surrounding hexes (the rim) just returned "mountain" (ironic, actually), grassland, grassland/hill, etc. The pedia only refers to wonders you can construct so I guess natural wonders don't exist (probably slated for an expansion, greedy bastards). Also missing great people. I guess AC didn't have them either but... yeah.
Lots of resources. I usually play Civ5 with abundant resources, but so far in a normal game I have a hard time saying "I should put a city exactly here to maximize workable resources". There's still some selection pressure but I don't feel it is as strong.
I don't like not being able to direct a city's next tile expansion without directly buying the tile.
The tech web doesn't specify whether a building unlocked by the tech is just a building or is instead a wonder. You can still kind of pick them out because it has a much, much higher production cost and usually has an obviously unique bonus (like free virtue, 'all x +something'), but IMO should be labelled explicitly. (This is obviously just a nitpick.) (I guess the aura around the icon also differs between wonders and buildings.)
Trade route management could be improved, such as being able to view active and available convoys from the overview as well as assigning them, rather than simply seeing what routes are in progress.
Civilian assignment in the city screen is a little crowded at the default zoom. It's easier to manage if you zoom in one tick of the mousewheel but the civ icons could do with being shrunk a little.
Likewise, selecting units in cities - particularly a sleeping trade unit - is difficult because they overlap and city label has a higher priority than the trade unit, obscuring it.
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Overall I find the interface very intuitive and smooth. I'm only 150 turns into a standard game so maybe there'll be more slow down, but I feel it loads faster and runs better overall than Civ5.