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.
1. What if it was uchiha kagami who did this (Possible Obitos father and the first Tobi).
2. Even Sasuke was able to go into Naruto and meet the 9-tails (Chapter 308 page 15). so why couldn't any uchiha have met the 9-tails before?
We have almost no backgroundstory at all about Mito & Kushina so it can be any uchiha that the 9-tails recognises. (Like Kagami).
3. How do you know that it is Obito or even Tobi, Madara is talking about?
"Him" could be anyone. maybe a mastermind behind it all(Kagami?).
He might even be talking about Nagato because in the previous chapter he did start out talking about Nagato and after he already named him why is it at fault talking about Nagato as "Him".
4. Are you sure Tobi gave Nagato the rinnegan? Tobi is clearly lying about alot of stuff. Like claiming he was Madara.
As i see it, there have not been any plotholes so far. Just a story that have not been fully told yet, I rather wait for that "Aha!" moment instead of just talking down on every chapter because i do not know the entire story yet.