Bravo!
Where do I begin...
I've been spending the last few days beating this game bit by bit. It was a terrific experience. The characters were likeable, the story - though a little confusingly set up sometimes - was solid and nice, the music was very good, the actual combat wasn't half bad and boss design was mostly solid. I was surprised about the actual length of the game, which when you pay attention to the story, spans quite some time.
On these points I have to compliment you and I hope to see more games of you in the future.
So. Praise aside, there were definitely a few points that could be improved.
Something that bothered me a whole lot was the cookie-cutter level construction. While you had a nice variation of enemies (who sadly looked very similar altogether) and bosses, the sheer amount of levels forced you to use them again and again. I understand that a game of this length is difficult to fill with vastly different bosses, but this needed to be adressed.
Another thing that bothered me a little was the way the levels looked. While you gave all of them a distinct feel, by adding different pictures in the background, it was sometimes hard to see obstacles because of that same background (that applies mainly but not only to the wood levels where you literally couldn't see the forest for the trees sometimes).
I want to wrap this up now and end on a high note, by saying that this was most definitely one of the biggest, most complete flash games I've seen. It had nice moments and even though the gameplay has a few minor issues, the story more than makes up for it. For that I give it the full score.