For your first flash game, it's pretty well done. I dont know flash well since I too am learn it, but i can make out some suggestion and some bugs i noticed. some bugs i noticed weren't many and not that major. when I get a "Game over", Enemies will fly down the screen, or the boss lasers will still appear. another is when Im in a boss battle (not Vaders), the laser will tend to hit me even when I avoid it. also when I align up straight with vader, hie ship tends to shake alot. that's pretty much the bugs I found.
as for suggestions, i would like to see more mission variety rather than gun down X number of enemies then boss fight. im thinking something to be more like vader, a sorta chase mission where you just have to avoid the lasers, or maybe some escort mission where another one of the characters can come in and help a little in the shooting. also, more enemy variety or at least buff them up at higher levels so it's more of a challenge. I would also enjoy to see maybe some kind of shop system, so you can upgrade the ship. and maybe you could do something about the Gaiaonline avatars as characters, you could get some art of them to replace the avatar.
Im trying not to make my ideas too absurd, sorry if this isn't much help.