Heres my ideas, I might repeat some of the other posters and I havent finished the game but here goes...
Docking and jump cutscenes as said earlier.
Money factor, have like extra non linear random missions you can do at any time during the game to get money to buy upgrades, repair ship and so on (GTA3 type stuff I guess), and earn money depending on how well you did the mission (mission ratings perhaps?)
Not sure if this is in the game yet, but decoys (I think thats the name) would be neat, where if a missile locks on you can use decoys to confuse the missile lock, like in another great game oh and also missile locking sounds would be great.
Make it more easier to notice when you being fired at, and hit, and from what direction, maybe its just me but I find it hard to notice when I'm about to blow up and die, maybe you could shake the screen, flash red, have louder hit sounds, and blow up panels and such...
Have a weapon gauge, to limit how much you can fire, and add full fire single fire type modes...
Make arming ships more complex, such as adding armour, sheilds, decoys, heat sinks, and so on...
Add a way to control the speed of the ship with the stylus, basically make it easier to control all ship functions with the stylus, currently its really good, but of course can still be improved.
Just some ideas to throw around, I'm really loving this game thou, great work, a sequel or expansion pack would be killer.