More diplomacy as always.
Buffs to orbital processing facilities.
Superweapon button in the planet menu.
On huge random maps, it would be fun to have each star populated by 1 or 2 factions rather then 5 factions in one star and 5 in another and 3 open stars.
In game real time clock and alarm. So often I lose sleep because I've lost track of time!
More setup options like starting funds/ships/etc.
Make the migrator not act like a combat ship (ie causing a radial point to display around the planet... always makes me think the planet is defended when its not).
More planet types like that mod thats out there. I just dont trust mods 100%.
Friends button while hosting a game. I can never remember the command to whisper to my friends, and while hosting a game, I have no way to contact them short of the public lobby. Perhaps an invite button would be useful as well.
More ship movement dynamics during combat.
Customize ship designs like in GalCiv2 (sorry, I got spoiled with that system

)
Other wishlist suggestions:
https://forums.sinsofasolarempire.com/304748
Ability to donate ships to an ally. Many times I have a surplus of ships in my allies area, but the enemy attacking him is an ally of mine so I cant help. It would be nice to donate those ships to his cause (for a price of course).
I do kinda wish that factions would stop requesting I destroy my allies units/structures/etc. To that end, it would be nice to see who is allied with who and who is at war with who, etc.
Espionage! Need I say more?