Alright, so Tobi was Obito. This means that Kishi is either a very, very linear author when it comes to plot, or he still has an ace up his sleeve for the explanation. If it turns out that he is just an extremely linear author, then all the plot holes we've discussed prior to knowing his identity are just really plot holes that Kishi left in the story due to whatever excuse. I have a couple of things I'd like discuss. If I didn't cover any other issues with Obito being Tobi, please politely point out any issue that needs to be explained.
>1. Tobi vs Yondaime fight
Issue: Size and skill. As of this moment, it makes no sense to me how Obito could have possibly went toe to toe with Minato and control the Kyubi at age 12-16. (I'm not sure what age he would've been, if you know please point it out.) I sort of suspected that there might have been two masked men during different times, and one of them fought Minato but I retraced my steps and found out the problem. Tobi used Kamui to fight Minato. As far as we know, Kakashi and Obito only have Kamui.
>2. Obito and Nagato
Issue: Age. I always believed that Nagato, Karin, and Yahiko were all older than Minato. The reason why I believed this was because I was under the impression that Jiraiya was Nagato's sensei before he was Minato's. If this is true, then Obito wouldn't have been born yet and this would make it impossible for Tobi to give Nagato the Rinnegan. Of course Obito could've lied to Konan, but I highly doubt it.
>3. Rocks on rocks on rocks
Issue: Anyone who saw the episode where Obito died also saw the blood splatter on the left side of his body. How could his eye have been saved? I've read a theory stating he activated Mangekyo Sharingan before he was about to die, then teleported the crushed half to the other dimension, but that seems a little farfetched.
So there you have it, these are some of the issues I see in the 599 revelation. Perhaps using an analytical perspective is too much for Naruto, maybe it's not.
Again, please feel free to post any other issues that need to be explained.
Note: If you feel inclined to respond with,"Let Kishi tell his story." then go ahead, but you've wasted your time. Everyone is letting Kishi tell the story, none of the fans have ever effected a chapter's outcome.