Read this chapter; it's quite interesting looking back at it. Here, Tobi says "Two of the six paths in the same being!" about him obtaining the power of Uchiha and Senju; and then about Nagato he said "You are the third path".
I really don't like this translation. The literal japanese makes it sound more like he's saying "Now there are only two people with eyes of the sage." And he's definitely not saying he's the third of the sixth paths. It's almost literally "Third Person of the great sage."
It's pretty much saying that Madara was the second person to become the sage(have the rinnegan) and that Pain was the third.
The more I think about it, the more sense it makes that he had three kids. Imagine it; there's essentially 6 Chakra affinities, and 6 "Paths". It makes sense that each child would inherit 2 Chakra types from him; the Uchiha inherited Fire and Lightning (Blaze), Senju Earth and Water (Wood), and the daughter Wind and Ying/Yang. Naturally, as time progressed, not everyone in the clan keeps those exact affinities as they mate with people outside the clan; but the Uchiha still has a strong Fire affinity, while the Senju has a strong Water affinity, and the Uzumaki has a strong Ying/Yang affinity or Wind affinity (not much are known about them other than their sealing techniques, really).
You went really out of your way to almost make up ways to get that to be 6 things. First off, those are not affinities. We went through what an affinity is above. Second.. you can't seperate fire/lightning, earth/water, and then not seperate ying/yang just so you arrive at the nice number of 6.
How can they be madara's eyes if pain had them? Don't forget he didn't always have the rinnegan (pain that is), and it's a little far fetched to think tobi implanted madara's eyes into a young boy for a insignificant town, with out any body even noticing a new set of eyes. This doesn't even take into account that madara obviously used both normal sharingan, ems, and rinnegan in the chapter, which means his eyes can go back and forth between them; something pain was never able to do. I don't think it's ok to assume pain didn't wake up one day and go "Oh hey, I have a sharingan too!" lol.
We'll have to look at the timeline more closely, but I think Madara could have been "dead" by the time Pain got his eyes. Also, taking into account that he can't go sharingan works perfectly if they were transplanted and if they weren't. Kakashi is another person who got his transplanted and he can't transform his eye back to normal. It's either full power or super new full power.
I'd have to say, based on what we've learned the past few chapters, Nagato HAD to have awakened the eyes after the attack - otherwise Madara would have been alive when he awakened them, which it seems like he wasn't. If he got the eyes AFTER the attack, then that supports my theory about Nagato being an experiment made by Madara to awaken the eyes in himself.
This makes no sense at all.
Why couldn't that "Madara" be the real madara and have the time/space ability? Oh, and also: why did the 9tails react to edo madara but never to tobi if tobi was the one who controlled the 9tails during the attack?
Kyuubi didn't give a shit about Tobi controlling him for a few minutes. Real Madara had him under his control for a while, back in ye yonder days. Why is it that everytime someone mentions plotholes with Naruto it's because they're incorrectly remembering what happened.
And really quickly, the person who attacked kohana with 9tails also met with itachi, and that's how itachi was able to set the amaterasu trap in sasuke for those eyes of whoever it was. That means, if it was real madara who attacked kohana, then his eyes have to be in fake madara - or else itachi wouldn't have been able to set the trap because he never saw the eyes. This means either A) real madara was the one who fought the 4th, and tobi took madara's eyes after he died(why the fuuu doesn't he have the rinnegan by default?) or B) tobi WAS the one who attacked the village with the 9tails.
We've known B was true and a fact for a long time now. I don't know why you feel the need to question it and even go as far as saying it's not likely.