Performing mocap isn't the issue with putting a 4-legged Motaro in the game. 2 people could act like a panto horse for that. The issue is getting his frame to work properly with the fighting engine. I imagine it would be time-consuming, but not impossible.
X-rays aren't the only stumbling block. Apart from the "bonuses" the bosses have (i.e. Armour, with no throws or Fatalities possible against them), every character, when not blocking, appears to share the same animations when they react to being attacked (e.g. Flailing about, rolling on the ground, somersaulting in the air, landing flat on their backs or faces, etc). Even the Shokan characters react the same way, with their lower arms copying the movement of their upper arms.
Motaro would need new reaction animations. Also, if possible, perhaps the other characters could have a shared X-ray attack, specifically for use when fighting him. Instead of highlighting the unique strengths of the character performing the X-ray, this X-ray would highlight a weakness Motaro has.
It's probably too much to ask, but I hope NRS would be willing to put in the extra effort required to add Motaro properly in MK9, as he would be a great boss character.