I think it's obvious that it has SOMETHING to do with the kyuubi chakra. Kishimoto has already stated that naruto won't have a lot of jutsus so I hope whatever it is that he'll be able to have many variations of it, something that'll have multiple uses, hopefully in offense and defense. Naruto swore off using kyuubi for powerups, kyuubi actually used naruto in that sense, even hurting him. It's different if naruto can actually use the kyuubi. The kyuubi has always been in someone, either that or roaming free, so I think naruto needs to take control of him eventually.
As for the whole genjutsu thing owning kyuubi, that's dumb to say IMO, because that's not really the case. Even if that's the case it doesn't matter when Naruto himself has been nothing but 100% useless against genjutsu so far anyway, so any powerup he'd get would apply to kyuubi as well... We've seen Sasuke break out of MS anyway cause he's all "powerful", Naruto will too when it's needed by PnJ