tl;dr: Its not possible due to multiple legal restrictions and programming restrictions and would be way more work than its worth.
long answer: PokeMMO remains legal because the program itself doesn't relate to Pokemon. From an outside perspective, the initial executable for PokeMMO is nothing but random lines of code that don't relate to or correlate to anything in relation to Pokemon. However, when ROMs are supplied, the program uses these ROMs as a base structure and then the program itself puts an MMO paint job on top.
This is cool and all, but presents a lot of restrictions and makes creating new regions beyond Generation 5 a pain in the ass. They can't create any new assets relating to Pokemon or else the game could be taken down, which includes cosmetics, 3D models, spriteart, etc.
Then theres the question of how 3D would translate to 2D, because playermodels have to stay consistent meaning either 2D character models would have to be used in a 3D environment like Kalos (impossible considering the camera angles that are used and would be damn near impossible to program) or 3D character models would have to be used in a 2D environment (which would be a huge eyesore and damn near impossible to program)
And this would all be done for what, 70 Pokemon? From a generation that wasn't nearly as well recieved as the 2D ones? It's too much work for too little payoff.