Naruto v/s Pain and Sasuke v/s Madara....
Ok, as Itachi said, he needs Sasuke's sharingan to prevent himself from going blind; exactly something that Madara has done in the past.
Madara is also interested in Sasuke to gain some eternal/permanent sharingan. This to me seems that Madara's plans are getting more sidelined and forming a separate plot-line that relates to the uchihas.
On the other hand, whatever plan Pein cooked up does not relate to himself or even to amegakure; but affects the whole world. His goal is often mistaken for "taking over the world" (this was part of his plans to hidan). but ultimately he revealed to Jiraya that he wants to "get rid of wars and pain" whatever means it takes (ultimate kinjutsu). Even his punchline of his ideals relate to Naruto (not the destruction part) and his past was similar in a way (he was an orphan; so was naruto and none of them had a very good life).
So I don't see the fight between Madara and Naruto (if that happens) to hold any importance over the fight between Pein and Naruto (if that happens). For Naruto, Madara (currently Tobi) is just an obstacle to get rid of (given Madara's background by Itachi). Whereas Naruto can potentially see his own image in the younger Pein/nagato during the fight (just like he related to Gaara and Haku).
On the other hand Sasuke has plenty of reason to see parallels between Madara and his brother and himself and Itachi. Itachi laid down the parallels flat out actually.
From what Itachi has said, Madara is turning out to be Sasuke's villain whereas Pein's background and ideals is making him similar to Naruto (or a very twisted version of Naruto)