Plenty of room for improvement.
The story for the game was good enough, and the full 3D environements were interesting, but the animation, graphics, and overall gameplay could use plenty of improvement. It was way too easy (if you can't get past the pipecleaner then you seriously suck). All that was required when it came to fighting groups of enemies was to circle around them, dodging their slow ass projectiles, and clicking fast. If you had maybe added in some cover and made bullets that were faster than that, it would have been less repetative and boring.
The music was ok, but it got pretty repetative aswell.
With the problems listed above, aswell as some glitchy graphics, the game winds up feeling very unpolished. I'm not sure how long you spent on this, but I think you need to spend longer on part 2.