I agree. The chibi is so kawaii. It would just look plain wierd if 3d attempted to be chibi.
Of course, if anime were in 3d, there might be some cooler BG FX. No more simple BG brightly coloured swirls of red and yellow. Although sometimes it adds to the charm of the 2d anime, i wouldn't mind seeing some buildings in the BG when charaters go in for a punch or a kick.