Everything definitely sounds great! Just a few things that I think might need a tweak:

I think the Plates should still only need to be touched once. Reason being that some Pokémon just don't have the hands to physically carry a Plate with them wherever they go. For example, an Electrode, a Dodrio, and a Serperior would be pretty out of luck. Also, a Plate, once retrieved, could be something the team could share rather than one player keeping it all to themselves. I would say if a Pokémon uses a Plate, they could still use all their original moves, but they just might not be as effective. Hence, that might be a reason why they might remove the effect. A Charizard that went water type might want to go back to normal if he came across a grass or electric type.

As for Arceus being the interceptor, I'm cool with that. I wouldn't actually make him blow up the world, though. It could just be a bluff to get others to take action. It might be a good plot point if the Master Plate falls into Schism's hands just for a short while before it gets stolen back. Also, I like the idea of Schism consisting of Shadow Pokémon. Heck, I'd be happy with the dictator being XD001 Shadow Lugia. That naturally seems to fit for the faction, and it would be a serious holy crap factor if he ever evolved, but I personally wouldn't have that happen.

I'm okay with dropping the genocide elements. We have a great plot and sweet subplots as is. What the teams decide to do is kind of up to them and what their teams goals are. Some teams may try to change the way of the world, though they would seem like the bad guys to a world of Pokémon who have always lived in a culture of violence and darkness. Others would simply want to be the new ruling regime. That depends and some of those goals could be conflicting.