My thoughts : Subtool grouping similar to PS layer grouping functionality. A texturing system similar to Mudbox or 3DC that works based per pixel rather than on poly distribution.
Totally. the surface tools were a step in the right direction. I still find it better than 3D Coat sometimes for retopo work. I cant believe theres no smoothed preview in 3dc.
Make sure your mesh is 100% true in the middle (reset XForm, pivot, etc) and set in the middle of the world. 3DC doesn't like it when a mesh is slightly bent on one angle or direction.
That trick (packing AO into blue) doesn't work with a lot of the best normal map compression formats (DXn, 3Dc, etc_ - because they toss the blue, store R & G at higher precision and reconstruct.
it's probably simpler to use 3DC and halve the texture size - I've done this and it works pretty well for mechanical objects that have normals with lots of smooth transitions.