@Zyphli:
You can animate the water easily depending on what kind of script you use for making the parallax maps. So far I've used Yamis Overlay Mapping script and Modern Algebras Animated Parallaxes.
With Yamis Overlay Mapping you create Overlays, not parallax pictures. You can still edit the map, but all the tiles will be invisible BEHIND the overlay pictures. But if you leave parts of the overlay blank, you can see these tiles.
In other words, don't add the sea to the map in the editor. Instead use the ereaser to make the sand coastline transparent, then it'll blend into the tiles of the editor, i.e. the water tiles. And these are animated now.
With Algebras Animated Parallaxes you create 3 different Parallax Pictures that cycle at a desired frame rate. So when creating the map, you do the coastline, the cliffs, etc. first. Then add three new layers, one for each step of the water animation. This will get you 3 different parallax pictures that are the same, except for the water. Use it according to the instructions of the script.
Here you'll also need a Fixed Parallax script. I think Yanfly has a "locked parallax" script that works well.
To have parts lying over the player, use pictures. One for each map. I think you'll need Modern Algebras picture fix for this.
Yamis Overlay mapping is easier to use imho, but it has some flaws with screen tinting. You are no longer able to tint the screen with colours only. Tints will only be recognizable if you add a lot of "grey".
Maybe the is a solution to this.