You could add a 'hard' mode where you can only play each level a max of 2 times before it's unplayable, or you stop giving exp after two plays.
Mines already on the field don't count towards using a weapon to kill someone (or is this intended?).
The wiping effect gets irritating after a while if you're going from sector 5 to sector 1 to get the every-weapon-kill-thing, a button for each sector might be better than prev/next, or removing the effect from those screens.
The team health bars should be out of the total for that specific team, not the team with the most health.
The 6th team member does not show up in (any?) maps, I spent several thousand maxing him and couldn't even use him.
I noticed that the timer slows down the longer you play, if this is from general lag, make sure you clean up all objects you're done with (no references. all event listeners removed for AS3, or removeMovieClip called for AS2), if it's not and it's from some odd timing issue (reusing a Timer in AS3 and accidentally adding time between firing?).
The camera constantly jerking around is annoying, I can't always see what I want to see.
Weapons sometimes go through enemies, or even entire plants, if your screen is large enough since weapon speed scales from 0 to infinity based on distance from mouse.
If you're using AS3, the team health bars should have mouse interaction disabled so objects underneath can receive mouse events.
(Character limit for comments forces me to split these into multiple comments instead of just 1)
Maybe if this was rewritten to use some semi-decent programming, and to run at a semi-decent speed when light is on the screen (9 FPS at low quality with no music? really?), I would consider rating it above 1/5.
http://img2.imageshack.us/img2/5965/lolpoorprogramming.png
 "Silent Conversation"){kind=icon}
 "Gravitee Wars"){kind=icon}
 "Armed with Wings 2"){kind=icon}
 "The Light Temple"){kind=icon}