1 - One thing that annoys me are rally points. I use them all the time, but ithink there should be some extra functions to them. For example, mid game, when i start using rally points: i order all ships from a kind (say, heavy fighters) to move to a rally point. That will send to the rally point both already built ships AND set planets building that ship to send them to the rally point; sometimes i want to rally the ships i already have, sometimes i just want to set planets to a rallypoint without changing the already built ships destination, but i cant do one, i have to do both at the same time. This happens at least one per game, and always makes me think "man, they should fix this".
2 - planetary governors
I LOVE this fuction. LOVE it. Theres just one problem. Why can you move improvements up and down in the governors quere build list if they wont obey it? I mean, i set a governor to build 2 factories, 1 farm, 1 happines building, and many markets, and when i colonize a planet and pick that governor, he queues 1 happines, 1 farm, and then mixes 1 1 market 1 factory 1 market 1 factory etc... The governor picks his own priority order, and factories, who are supposed to speed the development, are ALWAYS on the end. ALWAYS.
3 - more on governors
after you set your planetary governor to build things in a certain order, as soon as you leave the planetary governor editing screen, he will reajust the improvements on his list in alphabetical orderor sometihng like that (bu he wont obey that order too).
4 - even more on governors
The "CLEAR" button is WAY too close to the "DONE "button. I've erased my building lists SO MANY TIMES ALREADY!!!
Please, move that button away from the corner.
5 - I would like to see more info on the tactical zoom level. Sometimes its hard to see which planets belongs to who, or what kind of a ship youre facing (transports or military), so i zoom a little out 'till i get to the tactical zoom level. But once i zoom out to that, i rarely come back to the non-tactical view level. The game is pretty, planets are nice looking, ships are cool, but the tactical zoom level is so much more comfortable to play with. Except that it contais a lot less informations. What i would REALLY like to see in the tactical view is planet names (without having to hover my mouse on them) and turns-to-destination under my ships (so i dont have to zoom in to see how long until they reach their destination).
6 - Sometimes i send a colony ship to a distant planet, and forget about it. Suddenly, while im playing, after clicking new turn, a new planet opens up, and i have to set a governor to it, except i have no idea where that planet is located. Give us an option to move the game screen to that planet before opening up the planet surface screen. This would REALLY help me since i most play gigantic maps.
7 - Even better, (oh boy i would love this): when you colonize a planet, a pop up box should, pop up, and ask me if i want to pick a governor for that planet (from a drop-down list, without opening the planet screen), or if i want to edit that planet personally. Or at least make it possible to pick a governor from the planet main screen, without having to go to the "Details" page for each and every one of my 300 planets 
8 - LEASES. Ridicullous. "Do you want to pay 3000 bc, or do you want to pay 500bc + 100bc for 400 turns?" Reduce a little the cost of altermative leases options, or i wont even use anything other than "Terran Manufacturysomething"
9 - Make some way for us to manually heal a starbase. Maybe burn a constructor to heal ('rebuild') it, or money, i dunno...
10 - Make wormholes permanent, and not 1-time-use! That would be AWESOME!
I think thats what i want for now... Ill put something else later.