A few quick bits of feedback for you.
I tested the game on my ipad3 and it runs quite smoothly (it was the wrong aspect ratio and didn't resize properly, but that's probably due to you not having configured it specifically for larger iOS devices yet).
The first thing I'd suggest is changing the title, on account of the Star Trek First Contact film, as it seems a bit similar. The text explanation at the start went a bit quickly, and I didn't get a chance to read it all before it vanished (I think there were a few spelling mistakes, so I'll check this again when I get the chance). The Star Wars game comparison holds up, as it did remind me a little of the classic 3d game from the 80s.
I found the controls function quite smoothly, though I'd have preferred thumbstick style for greater manoeuvrability (a good example of thumbs tick controls that work well can be seen by searching the forum for Icarus Wave. I'd also suggest looking at Kronos by farflamex on Kongregate, as its full of ideas.
I really liked the pulse effect on the spaceship lasers, and the ship design works well. What I would also like to see is 'breathers' between missions, where you return to base and hang out in the bar, checking out scores and having conversations with other Npcs (wing commander style) as without the occasional change of pace the game could get quite repetitive (its possible that you've already planned something like this). All in all, its a fun shooter which doesn't yet bring any new ideas to the genre, though I'm sure you'll have plenty of opportunities to mix things up a little.
Best of luck with it, and let me know if you need more feedback on revamped versions.