GOOD news! I have finally managed to prepare development enviroment so I'm finally able to Compile and Debug your program. So expect more practical solutions (code samples) in future.
BAD news! After quick debug tracing through your code I see that there are several DANGEROUS sections (even if Asphyre engine doesn't manages to initialize you still try to initialize SpriteEngine which then fails as it needs already initialized Asphyre engine) which might lead to many bugs.

So what I'm gonna do first is study your code, try to find this sections and also try to fix them. Might take some time.
Then I'm gonna make some quick test to check SpriteEngine capability so I get some idea what we might be able to get out of it. This would probably largely affect my futurte suggestions.

As for the layers I was thinking about making a system which would alow you to use as many layers as you need (in editor you simply add new layers when needed). And if SpriteEngine is capable of working with thextures which also support Alpha chanell we might use so caled texture layering where you combine two textures to gain desired end effect. For instance:
Layer1: Contains simple texture which basically defines the overal colour of the water.
Layer2: Contains texture which has some parts semitransparent. This texture also controls water animation.
Layer3: Contains land texture. Part of this texture is transparent so water texture from below can be seen (shoreline).
So now we only need to figure out how much will each layer drop the overal performance (more layers more work for Graphics engine).

As for controlling the scroll speed I was thinking about storing the information about scroll speed in the TLine itself so that when you create specific line of sprites you also check if scroll speed should be adjusted.
Actually I was thinking about proposing you to implement some ingame event system with which you could contoll enemy spawning, maybe even change in enemy AI, scroll speed, and even controll sprites animations.
And when I'm talking about controlling sprite animations I have idea of implementing system which would alow you to easily synchronize animation between varios tiles and alow full controll on theese animations (stop them at any time, set them to specific position, change their speed, etc).
So you could have something like this in your game: Destroying a power statkion on an island causes all the lights to go blank, radars to stop turning, defensive turets to stop fireing at you etc. Posibilities are almost endles.

Yes yes implementing all theese ideas won't be an easy task but I'm sure it would be woth the efford in the end. And yes I'm preapred to give you a hand in all this now that I have development platform ready.

Wait when I'm gonna work my own projects