One thing I have taken in account, is when that bug where people would blow up when they loaded their save (not sure if its fixed or not.), vice asked for the save file, so for the files that are perma-death on, when you die, it should create a file that held all the same data, but is not accepted by the game. This way, you can still send your data to Vice, so he can fix bugs, but you still get that perma-death fun.
This next one is pretty minor:
New models. I've always hated how the shields, cargo bay and fuel tanks are just getting larger with the new ones. With fuel tank, it's understandable. Cargo should have one structure for the first, then two with attachment to eachother for the level two, then the third is infront or behind, sideways, then four all fitted in a square pattern, etc. Shields would be different, the level one shield should be a tiny machine that can be put pretty much anywhere, as if it'll have any effect, heh, next one would be two of them, the third would be a larger version of the first, but something glowing, to signify it is more powerful. The current one I personally think would fit the second last shield, as it's a bit large, but it should glow more. With the glowing should cause more visibility as well, so if you want to get in and out of an area stealthily, you gotta have the worst shield, as it emits the least light, and lets say they emit a wave, like a radio wave or something, and that makes it more detected. And for this, should be added (or modified, if there already is a stealth generator in the game), a stealth generator, instead of making you just invisible to radar, it should make you invisible to radar in range, the closer you are to them, the more likely they'll see you on radar. The shields would go against the stealth field, making you less stealthy, but a stronger stealth generator could compensate for even the strongest shield, but consume fuel or something. Or maybe energy, and have the stealth field toggle, this way when in stealth, you can hardly shoot, but can turn it off for a dogfight.
I don't expect these ideas to get in soon, (or ever, maybe. Although the roguelike one should be in, it's a toggleable feature.) but I would like opinion, I want to hear what you think about these ideas, any additions, or parts that you think would not be as great. (Most of you probably play the game a hundred times as much as me.)
EDIT: Pretty minor.. it took up twice the space of the original idea. heh.
[Edited on 12-19-2012 by Deliphin]
If that's true (about the stealth generator) then I've learned something new today ... and it answers at least one question. 
