Great graphics!! Well done.
I also died at the boss. I didn't understand if I actually hit him or not when i jump-shoot from afar, and a bit confusing that I couldn't use the special weapon while jumping. I think spawning bullets like cornelg7 suggested for both normal and special weapon would make it much more clear.
I also nearly got stuck when I moved to the wooden crate at the boss, as I started moving really slowly.
Right now the first level felt like a bit too much crouching. That could be related to the crouch animation being really slow. I think you should try to make crouching instant or near-instant and see how it works out, because I think the controls would feel much more responsive. Same goes with shooting, as there's now a small delay before shooting.