Using layers to separate animations in a file is a real workflow pain. Is there any chance of more Unity-like options for animation importing? Organizationally, it works way better if you have multiple FBX files--one for the skeleton, and one for each animation. Or at the very least, having all the animations in one, but using start/stop frames to divide them up into individual animations instead of using layers.
I suppose it would be kind of a pain because you'd have to introduce an import workflow that lets you choose frames or associate animations with a skeleton, but I think it would work much better.