Imo 3d collision and 3d models can be solved via events/js and addons, so there is less of a need for it. (still I am interested in the threeJS subset based integration you seem to be working on)
The issues that are more difficult to solve without engine changes are:
- 3d editor navigation to do 3d level design
- some form of transparency rendering pass
- more control over the shaders (maybe c3addon support for vertex shaders)