Nice list. I think you got most of the things that really stuck out at me from my first impression after playing the game. Just off the top of my head:
- Buildings/units too slow to build relative to tech rate, and/or don't provide enough benefits for their cost
- Great Person improvements (Engineer and Scientist at least) are vastly underpowered relative to their special abilities
- Logjams created through fixed one unit per tile, most annoying when a 3rd party wanders through a battlefield between you and another player, or when random wandering units block Workers from improving tiles
- Clunky and oversized interface, most prominently in the city build screen
- Several clicks and slow scrolling to enter diplomacy, why no one-click option like in Civ4?
- Preferences and options are immensely limited when you compare to Civ4... at least give us the options we had in the last game, e.g. turn off animations, regenerate maps, and a RIGHT CLICK MENU (constantly moving my units by accident when trying to cancel is a source of immense irritation for me)
- Keyboard shortcuts should be changeable by the user, e.g. "R" for both roads and resources irritates me constantly, and it's hard to get used to pressing "M" rather than "G" to move
- No info on how many turns to heal a unit
- River graphics are disgusting relative to the surrounding terrain
- Savegames not ordered by date
- Movie plays every time the game starts which is irritating, would be nice to have an option to disable it and just have a "loading" screen
- Lag issues between turns... of course they're present in every civ game, but it'd be nice to reduce them a little
That said, not everything is bad. I'm especially enjoying the combat side of the game, and the city states. Now we just need Firaxis to work on making the "builder" side of the game more fun/workable, and upgrading all the little details that they missed the first time around.