I haven't read these forums exhaustively, so I apologize if some/all of these have been suggested before.
Combat
I'd like to be able to toggle autofire independently per-weapon. For instance, I might want my lasers to autofire, but have my missiles be one-shot-per-click.
It'd be great if there was some way to sync or group fire weapons as well - I find that in the heat of battle I'm often too busy to babysit my weapons, and there are many combos that are completely useless unless they're fired back-to-back. Fast charging beams, for example, tend to be a waste of energy unless I can manually trigger them, as they typically require that I use some other weapon to drop shields first. Shields recharge so fast in this game, that it's usually a matter of seconds between them going down and them starting to recharge.
I'd also like some options for combat speed. Currently there's "paused" and "not paused" but some fights I wish I could take more slowly, and others take forever. One time I was more or less evenly matched to an opponent, but with a slight advantage. I fought with them for a good half an hour before I was victorious, taking no damage in the process. I pretty much just got up and left the game and came back some time later, which is not really the optimal way to play
Crew Management
I really need a way to label, rename, color, or otherwise tag my crew members to identify them quickly. There have been times where I've ended up with several of the same race and I find it hard to tell them apart. In one instance, I ended up with two identical crew members with the same name?! I couldn't find an option to rename either of my "twins." Color coding would be awesome, although there's not a lot of pixels per sprite to work with. Maybe a colored ring around their feet, and I get to pick the color?
I'd also like to be able to assign people to particular rooms or stations, and be able to tell my whole crew "battlestations!" or "to your posts!" - in the heat of battle, my crew tend to need to be mobile, but then afterwards I have to reset them all back to their default posts. It's also kind of a pain when I have to shift a whole room full of people around in order to get my "expert" crewman back to his station. Being able to assign him to that post and have him take priority when he's in the room would be awesome.
Navigation
On the system map, the rebels are constantly advancing. Normally I can eyeball how many jumps I have before they overtake a system at their current rate of progress, but sometimes the jump points are so close to the edge of their radius that it's literally pixels between me and total annihilation. The option on the map to toggle or display the number of jumps I have left (at their current rate of progress) before the rebels overtake a system would be quite useful.
Modding?
I'd really like the ability to mod the game, even if it's just that I can add my own events or change the parameters. I understand this might not be a priority, but it would certainly help me maintain my long-term interest in the title.
Other than that... this is a really awesome and addicting game, guys! I'm super excited to continue playing it, and I'm really glad I supported the kickstarter. Best of luck in the development process. I'll drop by again if I find or think of anything worth noting.