As in all Civ games the micromanagement is absurdly horrible. Unlike the the previous versions terraforming is simplified to the point that the auto-ai can do it competently. The "don't deforest" option really helps.
The build queue is as horrible as ever. Five cities with the same 8 item build order take 35 screen popups more than necessary and finding the right item makes even the actions requiring decisions a chore. How about a governor or a multi-city queue or just the option to remove from the build choices things we don't expect to ever build.
Then there are the unit commands. The low number of units per city and self-transportation feature is nice. Unfortunately, sending any number of units in one direction will cause the one unit per tile rule to bump the units and interrupt their preset multi-turn move. During combat I usually have pick location to move, shoot command, pick target for each ranged unit with an average of 6 of them. Particularly when siegeing cities Civ turns into a game of spacing puzzle.