A very nice piece of work
Most of the guns are nice (except for most plasma weapons, for some reason i find them mostly innefective)
Nice music.
Very nice gameplay, and the weapon variety is suprisingly big.
You should improve the ennemies, both in variety and strenght.
Biggest problem: LAG
Some suggestions that might help that (from someone who dont know much about flash)
Make some ennemies more armored/more hp so you can decrease their number on screen to help reduce lag.
For some reason, the lag is at its worst when there are dudes with guns, so, if it can be fixed, fix their problem, or just get rid of them and exange their place with superfast/super armored dudes.
And there was this little problem when you are pretty much maxed out later in the levels, when you get an upgrade that you already have maxed... the game gives you a random one instead... so if you pick up bullet speed when you are full it will change to anything else that can work (including nuke, healing or a different weapon! ARG, this last one caused my doom so many times!)
Anyway.
My favorite gun is the railgun; #16 in think (green ray of DOOOM!)