By my reasoning madara and co. cant effect naruto anymore. Their eyes let them control the kyubi's mind, not his chakra. They arent the same thing. When naruto is in control, his fathers seal is what controls the kyubi's will.
If he wigs out and lets the kyubi out, then they'll have an upper hand, but if he stays in control i think their just fighting a shinobi with an uber chakra supply. Thats what would make the 4th seem like a genius.