Despite the fact that you probably won't see this, this is still an amazingly solid game. The day you put this up it was in my favorites, and I don't regret anything. Hopefully you are still putting this brilliance into whatever you are on now years later.
Small bug I've found, if you click on survival mode without actually unlocking it, it freezes the whole game. Beyond that, a higher level cap (or for higher levels more skill points), a reset skills button. What you've already mentioned about adding in more depth to the story and levels themselves. Items would be a plus. Possibly adding in the ability to shoot a fireball diagonally. Overall short and simple. I like it.