This is really impressive!
This is, to date, the coolest 3D game I've seen in Flash. For a Flash game, the graphics look superb. The guns and enemies are well-designed, the engine runs smoothly, and I didn't experience any bugs during my time playing (except for bugs of the man-eating alien variety, of course). I also like that you included options to mute the sounds and music, though the music is a) good and b) changes periodically, both of which you get points for.
I only have a few suggestions for you to improve this game:
1) The textures for the walls could have been much nicer. I don't know if you deliberately chose something extremely low-res to improve processing performance, but they look muddied and generic. The doors, by contrast, look fairly sharp, and have a real 3D feel to them.
2) The mouselook/aiming system feels like it was designed for a Wii-mote. This isn't compiled in Flash 7, is it? If not, you can forget Wii players playing this. On the other hand, people with computers will probably find it somewhat irritating (as I did) to have the camera pivot when their mouse approaches the edges of the screen, and remain stock-still the rest of the time. I suggest opting for a traditional mouselook control: just have the perspective shift every time the mouse moves and keep the targeting reticle locked in the center of the screen. It would make aiming much, much easier.
Overall, great job. I look forward to seeing an improved sequel!