That was awesome.
First Flash game I've played through in a while. I only have some small construction criticism:
1) It's impossible NOT to upgrade everything eventually. It would be nice if there was some customization instead of being able to max everything.. but I guess you can still choose type of weapon, so no biggie.
2) The menus / mission intros don't fit the quality of the game - they look much less pro.
3) Most importantly: changing quality is disabled. Unless I'm mistaken, lowering the quality has little to negative effect with this type of bitmap-rendered game. Even on my awesome computer it was slow all the time in big fights - don't know if quality would have helped.