I think it would be really hard to balance the stats and abilities and stuff. There are a shitload of completely new Pokemon, as the Megas would propably have different checks and counters and stuff. Limiting this shit to one per team would be kind of an solution, but I am not quite sure about that. The 3DS offers the ability to patch games, doesn't it? So this might be a cure, if they discover that something is really OP. I would really hate the introducion of new Tier lists, just for those Digimon ripoffs :D