Consider: A mario and Luigi game with Wario and Waluigi in it
and the gameplay dynamic is you switch between controlling the two pairs during different story segments. The plot would be that something would intermittently possess mario and luigi and make them be evil, so princess peach pays wario and waluigi to be heroes in the mean time. The wario bros would have their own entirely unique set of bros attacks, more based around their own skills. Waluigi would have tennis, explosive, swimming and the like, while Wario would use his gas, his bike and of course call in some wario ware characters for aid.
Obviously the final boss fight is mario and luigi vs wario and waluigi, the two you control switching depending on which two are being possessed by evil.