Here's a bunch of suggestions, some of them seem to have already been announced, but i'll list them nonetheless:
United Planets: i'd like more involvement like the possibility to
-promote votes, as in to abrogate treaties (i hate when they limit starbase modules for example), or to form a UP military force to exterminate an evil civ/pirates or to prevent and give aid in case of galactic catastrophe
-bribery when voting UP resolutions (extremely useful if i can also promote resolutions)
-for minor races: they can ask to join UP and if accepted they can start to colonize new worlds (becoming in fact a major civ)
Military:
-possibility to invade starbase (i can invade a planet, why not a starbase? maybe with the use of a specialized module with high cost)
-minefields on borders of your empire (treaty option: to give minefield codes to allow free passage to friendly civs, these codes could be also subject to espionage but require a big effort to obtain)
-borders/possibility to threat civ trespassing/UP treaty banning out of borders starbases
-Invasion troops can be recalled after a conquest (as it is they simply vanish into thin air...), maybe gaining experience which adds to their hitpoints/effectiveness
-invaded planets: they should require a few turns to stabilize (aka get to normal production/approval levels), the sooner the invading troops leave the higher the chance they revolt, this being lesser in case my civ has high influence/nearby wealkthy planets, and higher if far away from my planets. Also for invading troops an "auto leave" option when reachen a user defined approval
-logistics of a fleet decrease allowing for more ships to join with experience, if fleet is disbanded the logistic bonus is halved
-ability to move military starbases(deathstar?) but extremely slow and can only defend when attacked
-tactical options when engaging enemy fleets as when invading a planet
-treaties with other civs to perform mock battles so to increase fleet's experience (less than real battles)
-given enough espionage, ability to target specific enemy ship subsystem to lower their effectiveness because you know their weak points
espionage/counter espionage:
-steal enemy ship designs to hit their weak points
-sabotage (generic or of specific planets/improvement given enough espionage level)
-bribery of enemy fleets/planets/starbases...
Politics/Diplomatic:
-given proper form of governement ability to have vassal states (they pay a fee, I protect them and they have access to my researches/economic etch bouses)
Miscellanea:
-stargates: even if obsolete they can be useful on huge maps (istantaneous travel): i'd opt for a tunnel approach:stargates A B con only go though tem, you can't choose C or D when entering A or B. they should also cost a bunch
-starbase modules to give economic bonus to nearby planets
-a multi constructor module (something like the adv troop mod) that gives the possibility to install eg 4 modules on a starbase with a single ship
-somewhat personalize fleets/planets: say i'm ethically good and do something evil: fleets/planets can rebel and join other civs, with a higher chance if they have great experience/wealth/influence (maybe for planets a decrease of income/productivity before defecting)
-terraforming 0 PQ planets or possibility to install special facilities to mine particular resources, maybe with unexpected events tha require more money/time to complete or a productivity penalty
-economy: a Galactic Stock Exchange (a galactic wonder?) which boosts your and other civs economy who decide to join (the one who build it has a bigger bonus)
-economy: a market place where you sell goods/ships/etc, other species can ask for contracts like "build me 10 fighters for XX bucks"
-random events/disaster that requires an UP emergency meeting
-some super-iper-mega-project as a dyson sphere which gives influence/research/manufacturing bonuses
-very huge maps (thousands stars)
-ability to continue playing even after a victory
-eye candy: an easy way to import leader pictures (the other day i wanted an elf portrait but had to desist)
Well I suppose this is enough