Obviously due to the short nature of the game and the fact that it's a prologue, the essentially non-existent story can be excused for a game that seems to want to have a compelling narrative.
In terms of level design, you certainly tried to keep everything fresh, not forcing the player to do one task over and over. However, with the exception of the grenade, you never really tried to make novel uses of the abilities. Everything was typical.
The boss fight was well done with enough of a difficulty to help give the end some closure. I liked how the boss battle changed as his health deteriorated.
The graphics are good pixel art, especially the girl's dialogue box and the boss sprite.
I'm not going to go into the controls, as a million and one people have probably mentioned the floaty jump controls. I don't think it's terrible since semi-floaty platformers feel different, but this is a bit too floaty for my taste.
Overall, it's not terribly memorable at this point. But this was just the prologue to an epic game, so I'm not going to judge the book by it's first chapter. You have all the programming essentially ready to make a great game, now all that is needed is to have more interesting level design and story and this game could make newgrounds history.
At the moment, though, I can't give higher than a 7/10. There's just not enough there to wow me.