It wasn't the controls that made the Metroid Prime games fit in with the series. Even if it HAD controlled like an FPS, it still wouldn't have PLAYED like one. It was the atmosphere, the exploration, the pacing, the weapons, the enemies, and the story that made this a Metroid game. Sure, I probably wouldn't have liked it as much had it controlled with dual analog sticks, but it still would have been an FPA worthy of the Metroid name.
Plus. even if MP3 controls like a next gen FPS on the Rev, doesn't mean that the next gen FPS will control like anything we've ever played before.