I'm pretty certain Pein has something to do with the Fuuma clan mentioned by Jiraya in c381. Why? Pein killed Salamender Hanzou. In Japanese history Hattori Hanzou was killed by Fuuma Kotaru in 1596 (as the legend has it), and we know Kishi blends in stuff from Jap history and (mostly) mythology. Please note that Fuuma in this case means "wind deamon". All the thoughts below are based on Fuuma comming from Whirlpool, which may be a loose term.
Naruto's mothers name is Uzumaki Kushina (meaning "whirlpool sheaf") and father Namikaze Minato (meaning "wavewind port"). Notice those names!? We know Kushina comes from the former Whirlpool Country. When this country was depleted is impossible to say, but my beliefs is that the Fuuma clan too is from the same country. It's very plausible that the country was destroyed in a war, and that it's people still kept on living in the same places, just in new countries, considering it's name. I believe this country covered Rain, Grass, Waterfall and parts of Fire.
Why?
Look at Pein different bodies' headbands as we see when Jiraya is flashbacking in 381. They are from Grass, Waterfall and Rain. Kushina probably lived in the part which now is Fire due to the fact she is Naruto's mother. Thats why I included Fire. Though she could have come from any of the other parts, the point is that she is from former Whirlpool.
Now, if the Fuumas are from Whirlpool it's very possible they had a relationship with the Uzumakis. It's only natural for clans to have ralations within the same country if they live in the same area. That means Pein probably knows a lot about Naruto as well. He acknowledged his power himself when Tobi ordered him to get the Kyubi.
We also know that Madara had the ability to handle the Kyubi's chakra, and that when the Kyubi appeared it was most likely his powers that summoned it. My guess is that whoever had Madara's powers (most likely Madara himself) tried to achieve the same things Aka is trying to do now. He had not taken Minato's skills in calculation, thus failed (Let's just call the person with Madara's power "Tobi" to not get into that "Tobi-Madara-Obito" discussion).
Minato must have known something was gonna happen again 'cause Jiraya doesn't seem to know why Kyubi was sealed within Naruto, but was certain there was a reason. Why Minato didn't speak of it may be his relation with Kushina, the Uzumakis' relation with the Fuumas, and Pein's contact with "Tobi". It's here my thought meets a dead end, 'cause it's impossible to say what this relationship was. But I'm certain that if all above is true, it has a major role in the Naruto story, and may explain a lot concerning the Uchihas. It links Minato to Pein as well. Pein controlls the Fuumas, and his/her superior seems to be "Tobi".
Then who is Pein?
It has to be someone Jiraya is familiar with. Pein said himself that he no longer had any love for his former master, meaning it must be one of his former students (as the frog sage also said). It also has to be someone who fits with Konan's character apperance. Why else bring up Konan? If all above is true Yahiko is a Fuuma too. Konan and Nagato are probably also from - at least in legacy with - former Whirlpool considering they live in Rain. This means the Rinnegan origins may be within former Whirlpool. What other connections do we know of within Whirlpool? Kushina! What connections had she that we know of? Minato and Naruto!
We're left with 5 options: Naruto, Minato, Yahiko, Nagato and Konan. It may as well be Kushina, though Kushina was never a Student of the J-man (or was she?).
There are 2 other unknown student of his, but since they've never been mentioned I don't she how it could be them.
Naruto is too young, Minato is dead (probably), Nagato and Yahiko is too obvious imo. That leaves Konan and it makes perfekt sense if you think about it. She seems mental, she is not a Fuuma and has contact with "Tobi" to settle her goals. Yahiko could be it to seeing how he came from Rain originally, but again it's too obvious. Kishi usually goes for the obvious though so it wouldn't suprise me.
The things that don't make sense now is she taking orders from the Fuuma, and that the only ones who has aged from the Fuuma is Yahiko. This can be explained though. Pein is Fuuma and Konan is the real Rinnegan user (perhaps Konan and Nagato). One Rinnegan's abilities is resurrection, and the resurrected gets the eyes. The piercings could be a way to contain them.
But anyway... 1 of the 5, Kushina or a new character is Pein...
Any thought on this (if you care to read it)?
Last edited by gjoerulv at 11:41 pm, Dec 12 2007
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I suspect that Kushina is dead.. So she can't be Pain, in my opinion..
She has no personality whatsoever~ I don't want the only Akatsuki female to be a sh*tty character.. 
Since Jiraiya first thought that too, but then in the end he says, "I know your true identity now, Pain!"
A completely new character?