1. I'd like to see map borders gone. It makes absolutely no sense to me that a ship that's slower than mine is somehow able to get away from me just because it crosses some arbitrary line, despite the fact that I'm right up his exhaust pipe and unloading on him with all my guns.
2. Better AI, "better" in this case meaning "more human". This goes right back to your point #1 but it's more than just that. Enemies seem to have an absolutely perfect awareness and instant reactions. A human being simply can't keep track of everything that's going on on the screen, all the missiles, fighters, laser blasts, and all the rest of it. Often I get hit not because I was outsmarted by the AI per se, but simply because I didn't notice the impending threat among all the other bright colorful pyrotechnics going off. AI ships should overlook things, fixate on their targets and ignore incoming threats, etc. This could tie nicely into the character and crew experience system, with low-level guys being more prone to such errors than high-level ones.
Not only that, enemies are apparently psychic and able to outright see the future, too. Observe:
I'm fighting a phase frigate and I'm about to fire on it with a pulse laser. Now the pulse laser doesn't fire immediately, it takes a moment to charge up, as indicated by the little progress bar at the bottom. The bar is about 2/3 up and the frigate's phase drives (or whatever those purple glowing things are) are already lighting up. There are bull@#$% reaction times and then there's dodging a shot
before it's even gone off.
Here's an example of a developer who has a pretty firm grasp of the idea:
https://www.youtube.com/watch?v=HaxiKobmAR8#t=1m4s3. More automation of tedious, repetitive tasks like buying and selling things. I'd like to be able to set my preferred 'loadout', for example, and just sell all the vendor trash, buy new supplies, fuel, and crew (or sell surplus thereof) with the press of a single Resupply button. A neat idea from Kingdoms of Amalur that I'd like to see is the Junk section of your inventory. You find something and if you don't want to keep it, you can just put it into Junk with a single click. Then you can sell all Junk at a vendor with a single click. I want to be blowing up spaceships, not shuffling little pixel art icons back and forth.