It's just the result of a natural progress. It's a lot cheaper to do 2D than 3D. For 3D you need X99 + 5960X + at least one High-End GPU. So that's a 2k€ Rig.
2D starts with a 150€ Board, 150€ RAM and a decent CPU which might cost 300-400€. So that's 700€ vs 2000€. It's pretty obvious that a lot more people will go for 2D because not everyone can afford X99 + High-End GPUs.
Rewarding special points just for 3D would shift the points even more to sponsored guys who can afford multiple GPUs without any problems.