-Was Obito's Kamui power an important part of Madara/Tobi's larger plan, or was it just a nice surprise? In other words, could a different eye or set of eyes have been used just as well, or is Obito's Kamui power special, important or unique?
-During the fight with Konan, Tobi says that he gave the Rinnegan to Nagato. How is that possible, if Nagato had those eyes before Obito was even born?
-Similarly, after killing Konan, Tobi says that the rinnegan "were always mine". How can that be, if Nagato had those eyes before Obito was even born?
-Also, why is it that Tobi claimed to have encouraged Yahiko to create Akatsuki, even though Yahiko was probably already dead by the time Obito was born?
-How did Obito change from believing that helping your comrades was the most important thing for a shinobi, to believing that hope was impossible and that world domination (including the massacre of his own clan AND a world war killing thousands of other ninja including former teammates and friends in Konoha) was a good thing?
-Why is it that Obito claimed to love Rin, but never once has Tobi mentioned her or asked Kakashi what happened to her?
-If people think Obito is dead, it would have been very hard for him to get into the Naka shrine to read that tablet. How is it possible that Obito then, having never been able to read it, would know secrets about MS, Bijuu, the Sage of 6 Paths, and Izanagi, that few other people seemed to know?
-Why would Tobi, knowing that Kakashi's eye had both a unique relationship to his own eye, and that it held a very useful long-range version of his most important kamui technique, never tried to kill Kakashi and take that eye back? If he's willing to go to war where Kakashi could potentially die, and if he's willing to fight Kakashi directly to the death, why didn't he ever do this sooner? Does he just not understand the benefits of long-ranged attacks?
-In order to unlock his MS and get Kamui, and to be able to become strong enough to fight Minato one-on-one, Obito would have had to be training non-stop from the moment that boulder fell on him. Even that might not be enough. How did Obito become so strong, in so short a time?
-Why didn't Tobi seem to know anything about Minato's space/time techniques, or Minato's speed, when he was on Minato's team and had seen his speed and FTG techniques in action during the war? None of that should have been a surprise to Obito (but was a surprise to Tobi).
-Why would Obito want to destroy Konoha, specifically? Why not get revenge against the ninja who attacked him, dropped boulders on him, and hurt Rin? If he didn't want revenge, why didn't he unleash the fox and take it away? Why would he have sent the fox to attack the village if he didn't want revenge and he did want to gain posession of the fox? What possible motivations would Obito have had to attack Konoha in the way that he did, at the time that he did? (Sure Kushina was pregnant, but she likely would have gotten pregnant again, if Tobi had just waited). Was it all just a ploy to cast suspicion on the Uchiha? And if so, what would Obito's motivation for massacring the Uchiha be?
...and the list goes on.
