Figure editor: I wanted to think about this before I replied before. First, I think that, yes, adding layers to it would be an improvement as rigging a skeleton can be tricky when there is lots of clutter. I would actually prefer, though, if the skeleton were its own layer in the object mode. That would probably muck up backwards compatibility, though it wouldn't be too tough to write a script to change the old format to the new format - run once per model and forget. Mostly I have to say that the figure editor is my least favourite section of Anim8or and I'd rather time be spent redesigning it, rather than adding to it. I'd rather see greater support for reusing and re-proportioning skeletons from one model to the next, more finite control over the weighting (influence sliders or alterable fields showing the precise degree of influence on each vertex), and a smoother control over the bones when positioning them. My thoughts, for what they're worth.
My other thought with the layers, specifically in object mode would that it would be useful to have a visibility priority level that one could set for each layer. For example, if I have a generic person model, wearing a shirt, with a necklace or backpack or sword harness overtop of that we would normally expect to see accessories over shirt over the figure. If you tried to build the three with separate objects then clipping and z-fighting is inevitable. Priority level would tell Anim8or to draw the back faces first, then overwrite with the figure, then the shirt, then other accessories or hair or whatever. For your consideration.