So, after playing the release version for a while, at least the following general UI items (ignoring gameplay items) are at least somewhat irritating to me.  Overall, a lot of nice work since I first tried it out.  Some of these things may be just my personal play style (I like very long games, on the largest galaxy size, etc.), and so I want to be able to move fast through things.  I tend to want to use keyboard shortcuts for speed, etc.

• Ship designer - Going to "User" tab, then clicking "Obsolete", changes the tab back to "All" (making it slow to obsolete a lot of User items)
• Ship designer - Sort by... something. Name? Class? Function? It's in order of creation right now (I guess) - perhaps sort options here would help.
• Colony Screen - "Cancel"ing work items fails to select the next item on the list automatically (making it very slow to cancel the entire workflow in a colony). Surprisingly, "Destroy"ing an existing itme DOES auto-advance.
• Diplomacy Screen - Declare War is very close to Trade, and has no confirm prompt for such a drastic action.
• Main Screen - Colony List - Using the mouse wheel to going through the colony list (or any other list) is very, very, very slow, even with the OS's mouse wheel speed turned up very high (the OS setting seems to be ignored).
• Main Screen - Colony List - Having options to sort here would be very useful (approval, class, etc.)
• General - Having some way to see or find where the Player Unique buildings are at would be nice.
• General - The "Escape" key should always go back one screen, all the way out the main game screen.  It does nothing right now.
• General - Double clicking a Starbase to select ships, then clicking Designer to change ships, then leaving Designer kicks you all the way back out to the main game screen, instead of to the Shipyard screen (where you would queue up the ship you just built)
• Govern - Commands - Upgrading a ship to to another gives no hint as to how much this upgrade will cost - it could send your empire very, very far negative.
• Technology - Researching a chain needs some sort of UI hint that it's possible, and someway to have that chain not always pick the top one out of all the 3 way choice options.
• Waypoints - If there's a way to direct an individual ship to a waypoint, I haven't found it yet.  (Keyboard "T" from GalCiv2 is not it...)
• Colony Screen - Chain clicking a number of the same item (say I do 2 factories, a morale research, and I flood every other tile with Econ items) is very slow in later parts of the game (a good half second or more of lag between clicks...) 

Hopefully someone from the dev team reads this.