I think there exists 3 versions of the Rasenshuriken:
1- The one where he uses it in close combat to engulf the opponent in cellular needles of death. Only usable in regular Naruto.
2- The one where he throws it while infusing it with Sage chakra to make it move and spin to create momentum, then when it hits is target, it expands into a huge shredding machine that will instantly tear you to shreds if cought.
3- A kyuubi version. effects are unknown but it certainly protects the user from the ill effects of the Rasenshuriken as well as adding it's own chakra to the attack.
I predict that he'll use the Kyuubi version in the fight against Pain because he just used the sage one and sage mode is over. Not to mention its the beginning of the fight.
In time, I believe when Naruto can use sage mode while controlling the Kyuubi at the same time, combine all of these elements into something called the "Final Rasengan" which is what i think Minato envisioned it will be used as.