If I remember right, Team Magma was more evil than Team Aqua. Archie actually helped you out sometimes, and I think convinced Max? (Team Magma leader) to help out in the end.. if not, then maybe they can make all three of you enemies, yet there's a superior team to Team Plasma which is kind of your friend. You know the saying- The enemy of my enemy is my friendYup, it would probably work something like Magma/Aqua did in R/S did too, assuming you can only get Reshiram in Black and Zekrom in White. If they did this though, I wonder how they'd pull off the good Team Plasma.