things id most like to see.
1) Open up the hard code just a bit to modding when it comes to both time related and random event types. i.e.
a) U.P. Voting - love to be able to set this to bi-annual, quarterly etc.

Adjusting the planetary colonization, random ethical event chances and Mega Event chances/timing. Mainly, to allow for creation of events that are NOT based on good/evil, and to allow for easier testing of such. (erm, is it possible to trigger an event based on planetary population?)
2) U.P. votes should have a 1 month warning, allong with What the vote will be - therefore allowing for more political options.
3) Minor Races.
a) please, at least in the scenario mode, allow for the minors to again be able to colonize, or allow personality adjustments for the minors that does not turn them into a "major race".

Minor races of the same ethical attitudes should be very inclined to ally with each other early in the game, thereby increasing thier survival rate. Think of them as minor political factions within the UP, a "Confederacy of independant planets" if you will.
4) Remove some of the Hard Coded referances on various improvement types throughout the game to allow for more modding options. i.e. F-LogisticLimit currently requires specific building types to be used, effectively cutting it off from modding.
5) Yes, please create a new govener that allows for Planets creating Y ship, go to Z Rally point - would be amazingly useful.