1) When multiple constructors will arrive at one starbase in a single turn, have a field that displays the number of upgrades selected/available, checkboxes to select the upgrades, and a running total of additional costs, with just one confirmation at the end.
2) When loading a game, don't display the same message you get when you start a game, it just doesn't belong there at all and looks, well, rather dumb.
3) In the list of ships you get when you click on a fleet, have an upgrade button for each ship so you don't have to break up the fleet into separate map squares and upgrade each individually before reforming the fleet and continuing on...much too much tedium.
4) A built-in feature that will not let you play at all past a certain time, which you set once and cannot change without calling Stardock tech support, on Sunday-Thursday evenings
5) Ability to launch transports and colony ships with zero soldiers/colonists.
6) Ability to "launch all ships" or "launch all of a specific category or type", for instance all colony ships, all transports, all constructors, all warships.
7) Ability to customize the colours of all races in a game without "modding".
8) Ability to set all players to be custom races of any choice, to test your race selections against each other.
9) Instead of tabs for military vs. social starbase improvements, just have a checkbox that would put all military first, or all social first.
10) Ability to set all planets (even planets which don't yet have a starport, so they will being building them immediately after the port is finished) to building one particular type of ship, either repeatedly, once, or until a certain number of the ship are completed. For example, if I need 60 constructors to put a wall of starbases up along my border with the Drengi, I can say "build 60 'Constructor 12pc lr' then return to previous build instructions (or not)".
11) Instead of the above, create a "build queue" for starbases, so that as constructors arrived, the assigned modules would be automatically built. The option could exist to prepay for additional-cost modules, or have the "are you sure" popup appear as necessary.
Edit: 12) and make dialogs/popups movable so I can move them off to the side, even partially off-screen if I have to, to see where the heck I am in the galaxy when I need to!