Mr Sinister as the opposite of Stryker's group in the second movie. A human obsessed with mutants and wants them to replace humanity or at least become the dominant one of the species. He'd be Xavier and Magneto's teacher from decades earlier whom both split off from (though Magneto was somewhat more influenced by Sinister than Xavier was). He'd play both sides in that he also has a second life as Nathaniel Essex, to whom the government had been looking to for research on mutants (he was working on mutants longer than Stryker) for decades. His interest in the registration program (which he was a proponent of) would be so he could identify the stronger mutants and have access to them (he was aware of Stryker's plan and wanted the registration to suceed so he'd hold the stronger ones under his control and shield them from Cerebro II and unleash them on the world after Xavier and Magneto were dead).
Of course, this would all be "too much" for audiences...