I found an odd bug where placing facilities on your planet can sometimes make buildings you have not bought/built yet disappear, oddly enough they reappear if you change tabs. Also I find that the scroll bars on the menus are too skinny like toothpick skinny, yes we have mice in this century but why have scroll bars if you can hardly use them?
Regarding space battles, I know I know its a beaten horse topic but here is my idea. Why not have something like a turn based battle system instead of watching it on auto pilot. You could que up a set of random actions on your turn then watch how they play out in real time.
The other idea is regarding a mission or quest system something similar to Spore where your captain can pick up random missions from your home planet in order to complete a series of tasks, nothing big but perhaps it could tie into discovering ancient technology/relics.
Some ability to hire mercenaries, this could have an interesting mechanic to it imagine another race willing to pay more for the mercenary you hired and used them to back stab you. Also an ability to grow your commerce by outsourcing your trades off world.
A time line step ability, instead of mashing the keyboard to pass the time. What if you could control time the way you control your television. This could also incorporate an interesting feature where your choice to reach say a level three tech tree could impact your decision in the manner that while your doing one thing through that timeline your opponents or other races have also made certain decisions. So the choice to play with a time line or accelerate time could have dire consequences or interesting advantages.
A galactic auction where you can sell your ship designs to other races willing to pay the most, this could have benefits for example if you designed a ship with two lasers and launchers and one guy buys it. You could end up buying a design much better or worse than what you sold for more or less the auction price. Also if the proponents felt cheated they could later take action by either demanding a return or going to war.
An ability to create/destroy your own planets once you have ascended I mean if you become a type two/three civilization it only makes sense.
How about adding defensive weapons to the ship editor, something to protect your borders with. Stuff like turrets, cannons, batteries etc..
The infamous cloaking device 
The ability to create a mothership in the ship editor that has an extended slot for adding virtually anything within reason. Think Homeworld, but more like a multipurpose ship that can do every task you would otherwise spread between a fleet of ships, it could act as a flag ship for your fleets or be used to protect your boarders/homeworlds.
