Well if you're importing it all as I suggested I can't really see any problem.I don't have or use AE but as I understand it, it's PhotoShop in motion which I do understand. If AE in fact has all the layer adjustments available that there is in PhotoShop there should be little you can't do.

 Things like the file size of the ecosystem should only be a concern in Vue5Inf where actual polygons are involved. As you are only importing multi layered image files I would assume that your frame size[800x600] and dpi [72,150,300,etc.] are the controlling functions of size.

Haven't played with the water yet, and don't know if I can check the pre animated water out as lots of stuff is disabled as it is a demo after all....still an encouraging look. But if you can make it flow in Vue, the the frames you export to AE will be flowing...no?

 

Once in a while I look around,
I see a sound
and try to write it down
Sometimes they come out very soft
Tinkling light sound
The Sun comes up again