The Kyuubi has only ever been completely subdued and controlled by two things:
The Influence of the Mangekyou Sharingan
and
Hashirama's hidden Bijuu-Controlling Abilities.
If you think logically, Naruto is already lost. The Nine-Tails' Chakra is uncontrollable by him alone, and in the 6 Tailed-State, he is completely unconscious.
Unless we infer that Itachi's gift is the Influence of the Mangekyou Sharingan upon the Kyuubi. Not Naruto Possessing the Sharingan, only the influence of the Mangekyou upon the Kyuubi...which would provide Naruto with complete control, even in the Kyuubi's Manifested 9-Tailed State. The bones we all know for a fact are the first stages of Kyuubi's physical manifestation from pure chakra to a solidified body.
As for Yahiko Pein...again think logically...even if Pein is on a completely different level than Orochimaru was, the 6-Tailed Fox knows its target and will stop at nothing until it's destroyed. Yahiko Pein's body will be destroyed within the next few chapters of this manga.
Nagato, if Yahiko's body is destroyed, will snap even futher into his warped idea and will decide to go after Naruto himself...only to result in his imminent death from a mixture of Chakra depletion and the Kyuubi's Rage.
or..
as stated in an interview with Masashi Kishimoto himself,
Killer Bee will invade Konoha AND will kill an Akatsuki...one will go blind.
The only reason blindness is issued in this interview is for two separate doujutsu. The Rinnegan OR The Sharingan.
Either Pein himself will go blind from a surprise attack by Killer Bee
OR
Sasuke will go blind and be forced to receive Itachi's eyes, which Madara has placed in a container.
As for Madara's plans, he may believe there is something higher than the Eternal Mangekyou, otherwise..why else would he have wanted Sasuke to take Itachi's eyes? In my opinion, he hopes to find the next/higher level of Sharingan through obtaining ANOTHER set of Eternal Mangekyou...only my opinion though.
As stated by Kishimoto, 3 of Naruto's Important People will die...here's your list:
1-Jiraiya
2-Pa Toad
3-Hinata
She won't be back, but will be missed. She was a main character and prospecting love interest for Naruto. In the 1st half of Naruto, we grew with the characters..but in Shippuden, the Archetype is taking place...the real plot. This is undeniable, you may wish to deny it and even state that I'm wrong...but what I've said in this paragraph may as well be truth.