Plot holes I have noticed:
1: Obito got crushed by the boulder and died (Kishimoto got around this by having Obito activating his Mangekyu Sharingan before he had obtrained it...)
2: Tobi infiltrated the leaf village, killing dossens of ANBU black ops, summoning the Kyubi and fighting toe to toe against the 4'th hokage (all this happened a very few years after the bridge mission where Obito was supposely "crushed/killed") at this point Obito is still in his mid teens/late teens! (14-18) So when did he get this massively powerup? and the huge amount of information he got... and more importently how? and many skilled ninja train all their lives and still dosen't become as powerfull as Obito managed to be in just 2-5 years... He pretty much went from being a loser/guy without much talent for being anything more than just a cannon fotter ninja (with the sharingan though) to becomming one of the strongest characters in the naruto universe! (Kishimoto never got around this plot hole, it's still there, unexplained)
3: how could Minato not reconize his former student, sure as far as Minato knew he was, but Naruto said himself that when Shinobi get to a surtain level they get the ability to instantly know/sence the other person they are fighting, and know their fealings, thoughts, skill level and desires as soon as they fight with them (naruto says this after the incident where sasuke tries to kill sakura, kakashi and Naruto) (Kishimoto never got around this plot hole, it's still there, unexplained)
4: When Kakashi died he saw Obito in the "next world" as a Kid, so how can Obito be alive and a adult in the real world, when his "soul" is in the "next world" as a kid... ?
5: Obito obtained the Mangekyu Sharingan after Kakashi killed his closest friend (Rin) .... and here I though that the Mangekyu Sharingan only got "unlocked" when you personally wend true the traumatic experience of killing your own "best friend" (this was how it was explained to us) not magicly getting it when someone else "who do posses 1 of your eyes" killes their best friend. (Kishimoto explained it this way... I personally feal it's a copeout, and it was his only way of giving Obito the Mangekyu Sharingan without having Obito kill Kakashi)