*Very long post ahead*
Motaro should be immune to throws and most projectiles. Some characters' attacks' animations should be altered when done on him. As for X-rays, either they shouldn't be doable against him, or they could give certain characters unique X-rays to use on him, if their regular one couldn't work animation-wise.
As a playable character, if he had to be weakened a bit, then he'd only need to lose his immunity to projectiles. That plus X-rays being doable on him would make his playable self just vulnerable enough not to overpower him.
As for fatalities, I think they should either give Motaro unique death sequences when he loses, which would differ depending on the characters.
Sheeva, for instance, should skin the front of Motaro's body, then jump behind him and tear the rest of his skin off.
Scorpion could do his throat-slitting and torso-cutting fatality on him.
Some fatalities however would only need minor tweaks when done on Motaro, like Ferra/Torr's (Ferra could just cut Motaro's human half in two instead of his whole body), Kano's (just have him standing on Motaro's back), D'Vorah's (no tweakings besides Motaro's skull), Quan Chi's (at least the sword-swallowing part) and Kotal Kahn's (no changes needed at all).
It's either unique death animations per characters, or giving them more than one fatality to use on him. The latter would take a lot of work, and the former is already asking a lot. In likelihood, he'd just drop dead after defeat, like he did in MK3, sparing NRS even more headaches than the one they'd get just working on his gameplay.
Finally, for brutalities, again, some would only need minor tweaks, like D'Vorah's chest-bursting one, but they'd probably have to create some new ones for most of the roster. Another reason why they might prefer to just not make brutalities usable on him.
So to conclude, if we're being semi-realistic here, then the best we could hope for are some tweaked X-rays and animations when fighting him, or a complete immunity to X-rays, so the only way he might work as a playable character would be to make him vulnerable to projectiles, like I already suggested.
