Sharingan cannot see through shadow clones. When Sasuke said he could he was most likely referring to knowing Naruto and his tactics, thus "seeing" was a metaphor for interpreting movement and strategy... and he was wrong.
It is entirely possible that the real Nagato was summoning the statue while pain was off. Unlikely though because I am starting to wonder if pain is not using the machines we saw in the rain village to create and/or aplify his chakra control ability. More interesting with Pain is when the corpse puppets seem to exhibit signs of individual personalities. If they are being controlled... Or perhaps to lessen the strain on himself, he only shares vision and thought with them and allows them to move more or less on their own. To counter that argument I see coming, he trusts them because he animates them. Without him they all die... again. Or perhaps, Jiraya remembered many of the bodies. Maybe Nagato bore a grudge and collected corpses that would desire revenge. "Swear fealty to me and I will not only breathe life into you, but help you claim revenge on the Shinobi who stole your life."
Tobi is Madara.... NOT OBITO OR DANZOU!!! The only evidence anyone has ever had to support this crazy theory was the eye thing. So what. The real reason Tobi covers one eye. That mask makes it real hard to notice he has Sharingan, and considering there were only two sharingan known to the world, now one, it would of made people ask questions and possibly learn the truth of Madara. Not to mention the fact that he's roughly 50 FRIGGIN YEARS OLDER THAN OBITO!!!! Although... if Obito IS alive (he's not) than we can put to rest the is Kakashi dead thing. No way Kishi would allow him to die without knowing the truth.
Course he's not dead. Why show him talking to daddy if it doesn't matter? He'll be back. Right after daddy reminds him he's being selfish and still has duties to perform. He'll be beat to high holy hell, but he'll be back.
Saw a comment when someone stated that Pain used an eye tech on Naruto before stabbing him..... No he didn't. Far as we've seen, he either has no eye techs of that nature, or thinks they are beneath him. Naruto was stabbed with a chakra rod. Same thing the Pain's are pierced with. That was Nagato trying to assert a measure of control to keep him from fighting further. Course that means Kyubi will be pissed, Naruto will say I got this, Kyubii will say F you kid I aint dying, than SAGE FOX NARUTO!!!! Ok probably not. But high likelyhood Kyubii will help Naruto fight off Nagato.
Word