I think the main problem is the views of differing countries, im sure Japan would essencially boycott a game where you played the Bad Guys, but extremely more so if it was Pokemon game where you played as a Bad Guys, but the thing is that Team Rocket has firmly stuck itself into the main series' canon for so long now, Team Rocket probally wouldn't work as a- lets say- Tower Defence game.
If anything, id love it if they expanded into the game's universe through alturnate genres or somthing besides making themselves detatched from the canon anyway (Pokemon Link/Trozei was more detatched from the canon than say...Pokemon Ranger, however. Mystery Dungeon doesn't really have much of a canon, the 2/3 main trios/duos of their respective sequals are dissattatched from eachover plus the timeline is too far in an apocalyptic future that you can't tell where it begins and where it ends)
How about a hack and slash game where the main character is in a time where Pokemon arnt kept in ball's and they're misunderstood creatures that could cause bodily harm if harmed? would be sort of a cross between Torchlight and Pokemon Ranger, eventually you discover you have the power of Aura, stop a War and perhaps manipulate Lightsabers.
