Lets just talk about how a Team Rocket pokemon game would work out.
the story would follow you as a newly recruited member of Team Rocket, with the main goal of growing in rank until you are the main leader. the setting would be when Giovanni first went missing. once you finally reach the highest rank, Giovanni would return resulting in you battling him for power. in the end, you may win, but all of Giovanni's loyal guards would kick you out anyway, making your character Quit the gang life and return back to your hometown, pallet town, to be a professor for the rest of your days.

the combat would be very similar to the pokemon games in the sense that you would still fight wild creatures, but you would be restricted to Team Rocket approved Pokemon. another mechanic that would be introduced to differentiate it would be squads. like i said, you would rank up in power, and when this happens you get other Team Rocket members to follow you around and help you assist in battle. overtime, you would start to use more and more people to take on larger batches of Pokemon, with each person you have containing two or three pokemon of their own.

That'd be my take on the game. feel free to argue or add on, because now i'm pretty engrossed into the idea of a Team Rocket game