wanted to think about this when I read it, and
kind of missed it until now.
considering it, I don't see this as that
likely a scenario, after all Madara was blind when
he took Izuna's eyes, burned up eyes
regenerating doesn't sound quite right. If it
was as simple as just switching them with each
other, I think that would be what all brothers
would do out of habit.
Ok to throw in my two cents. They mentioned before
that the Rinnegan always had to have a host, so by
seeing Nagato as a young boy with the eyes would
mean that Madara had died around the time he
received them. So IF Tobi is a clone, then why
wouldn't he possess the eyes instead being
that Madara would have had to make said clone
before death and would have passed his eyes on.
Now I also have noticed and like the points people
have brought up about his eye never changing, so
to me that clearly means its an implant. Another
reason I doubt it is a clone is the fact that
Nagato at one point agreed to help him, I
don't think he would be submissive to a
clones will instead of taking the power for
himself, which I feel he could have done.
I also have a problem thinking that Nagato would
be used to revive Madara's body anyway. If
Nagato could revive anyone from any point in time,
why wouldn't he sacrifice himself to revive
his friend instead of a stranger. I think that is
because his revival only works on recently
killed... or else there would have been a lot of
revived people from the Konoha cemetery
Though we were told
Obito's other eye was crushed, I dont recall
anyone ever saying that when they buried him the
eye was completely destroyed 100% so perhaps the
reason he has similar abilities to Kakashi is
simply due to implanting the second eye
(Obito's) into himself to either pose as a
Uchiha or to simply get his powers.