Awesome
its a very very fun game to play, here's a few ideas to help make it better.
I think you should remove these "miss" things entirely. Having to blow up after a certain number of ships fly by is NO fun, especially since when you respawn you are for a few seconds invisible (not on screen), and so many ships get past you at that time.
You don't lose a life when you kerplode because of misses, I don't know if it was intentional (I sure hope it was, cuz I don't think I could fight the last boss if it wasn't), but again, definatly remove this whole aspect. If you do keep it, keep it merely for score sake. This especially rings true when you overheat your weapons, this is a gauranteed "blow up" situation, as at least 30 ships fly by you by the time you cool down.
The whole level up thing was really well thought. After you reach a certain score interval, you're ship levels up with new equipment, and new enemies come in. I enjoyed the enemies, pretty neat variety you got going on.
Definatly change the shoot buttons to Z, X, C, or something very close by. I kept forgetting ctrl was the blue shot, and shift the normal shot.
Very spectacular graphics, loved it all.
Aside from other upgrades other then shield and heat, nothing else to add.
Very well done.