That was cool!
Your hard work has paid off man, because this was really enjoyable to watch! I really like where the story is heading, but I'm a little unclear on the plot. But that's okay, its my fault, I should of read through the beginning part more slowly and cautiously. I'll go read it again.
I couldn't suggest any way to make your animation any better because it was really well done. Changing the camera's perspective occasionally was done nicely too! But I think the way you assembled the sprites together into a beautiful environment was one of the most interesting things to look at. I'm just curious how the next episode will turn out now!
Just one thing though. Splitting the episodes was obviously done intentionally, but is there anyway you can put it into one part? Putting scene selection may be a bit more important than you think. And besides, your Flash movie would seem more impressive if you could have scene selection.