I like that you started with 3D and ended up with it; I started that way too. The screen resolution is too low for a shooter; sometimes the mouse focus disappears, shader freezes aren't easy to fix on the web, and sounds are absolutely essential. Regarding the art, it's perfectly fine to use base meshes, but consider using assets if you're not modeling. Also, regarding bonuses, it's not a big deal, but you shouldn't have used static collisions; it would have been simpler. Regarding the gameplay itself, scoring points is a bad idea; it would have been better to just make one linear level.