It doesn't change the fact that for each simple recolor, there's a dat needed, and the size can get big rather quickly, so 3D really is the way to go. critter frms aren't fun to work with unless you're a masochist.
Wait, you don't mean about setting FOnline on 3d engine?

In current case, i don't deny that new critters with complex frame art require a more efficient creation method. A rigged 3d model with replaceable textures is, in this case, an ideal solution. But it doesn't remove the necessity of postprocessing the render images into the frame animation.
I believe, it would be more convenient to work with a spritesheet instead of single layers.
Plus, i offer you a solution to
recolor the whole frame set in one passage for such colour-homogeneuos image, as in this case, a Bluesuit. The result could be seen in my previous post and can provide some colour diversity for the start. I'll try to make some more at Sunday.
And that's by throwing all frames together on one sheet, replace the colours, cut it down again in frames and import. It's still much less work than working on each single frame, switching between layers.