It's shaping up to be pretty great already, but I'll do what I can to help you improve. Everything looks pretty clean and nice here - though it's still not perfect.
You should change the water's color to be a more orangeish color, so it suits its surroundings more, and I think the animation would look much more smooth and nice-looking if it was about half its current speed.
Also, the way the Layer 3 clouds scroll vertically when the screen scrolls looks pretty weird. If you're not able to change that, I'd recommend just removing the vertical screen scrolling entirely. I'm not sure if you'd have to sacrifice some of your personal plans for that, though, but do as you please.
I'll keep an eye on this hack.
aran - Graces of Heaven