Plothole Number 1: Tobi’s Power Level (chapters 500-504).
There is no way Obito could turn into an alpha dog shinobi who mastered S/T phasing and teleportation within a 1-2 year time frame. At 15 years old? No way... There is also no way Obito would know how to extract the Kyuubi, hypnotize it, control it like a puppet, and then summon it wherever the hell he wants to. And all of this is supposed to have happened 1-2 years after Obito supposedly died? That’s just not feasible.
Plothole Number 2: Kyuubi recognised Tobi (chapter 501 page 8).
The Kyuubi actually recognises Tobi and possibly knows who he is. If THAT doesn’t convince you, nothing will. The Kyuubi made a direct transfer from being sealed into Mito to being sealed into Kushina, so there is a fundamental contradiction for the Kyuubi to recognise anyone in the outside world when it was sealed for all that time. If the Kyuubi actually recognised Tobi, it means Tobi has to be someone who was alive during Hashirama/Madara’s generation.
Plothole Number 3: This is HIS doing (chapter 560 page 2).
"This is HIS doing." That means Madara knows exactly who Tobi is, but there is no way Madara could have worked with Obito because Madara had died already. We know this because by the time Nagato gets Madara's Rinnegan from Tobi, Madara is officially dead - "I awakened these eyes shortly before my death." (chapter 560 page 15). This is important because Nagato is older than Minato, and Minato is older than Obito.
Plothole Number 4: Nagato is much older than Obito.
Why is this important? Because Tobi GAVE Nagato the Rinnegan. In other words, it is impossible for Obito to have given kid Nagato the Rinnegan because Obito is much younger than Nagato.
