Good question! What I can tell you is that, according to a Team Rocket member, turning people into furries will 'create massive amounts of energy. Enough to easily take the world.'

There's presumably some sort of intermediate step between 'generate loads of energy' and 'TAKE OVER THE WORLD', but it's never made clear. I'm also not entirely sure how merging people with Pokémon is supposed to generate energy. So, yes, there are still a couple of '???'s in the agenda.