Have you considered that maybe Tobi was telling the truth? We know for a fact that there was a "masked man" who we assume is the same "Tobi". So the current Tobi denies attacking the hidden leaf 16 years ago could that not mean it was someone else at the time? He knows fully well exactly what happened but denies it was him for what purpose?
The only flaw in thinking it was someone else was the s/p kamui abilities used at that time linking both that masked man and Tobi together. The only real answers to come from that is thinking that someone is using obito's eye back then or someone holds the same ability as kamui (very unlikely). If infact lets say kagami/izuna we're related to obito would they have a chance of having the kamui ability in their family?
I find it virtually impossible for anyone to have progressed so far in 3 years. Naruto our main character who has shown to have one of the highest progression rates learnt odama rasengan and improved his skills quite a bit over 3 years with jiraiya. But he was quite decent before that considering he'd taken down gaara. Even sasuke over 3 years with orochimaru become much faster, skilled with swordsmanship and his usage of chidori. However neither of them could progress as much as obito "apparently" did. Even with madara as a mentor, there's only so much he could awaken for him. What "best friend" would obito of had to kill? I doubt he'd kill rin unless he was completely mind ****ed but if he killed rin, what is his motive for hating kakashi? How is he able to use his kamui without activating the sharingan? These things not even madara or itachi have been seen to be capable of...
The Tobi who formed the akatsuki and groomed nagato and yahiko into becoming the founders and the tobi who fought minato CAN NOT be the same Obito-tobi we see here and now. However, the tobi who met itachi had long hair and almost definetly possessed,as the kages said, "kotomatsukami" (sorry if I spelt it wrong0. Which is shisui's ms ability which was used on the mizukage/3 tails jinchuuriki yaguura. So the long haired masked man has shisui's ms ability... Was it shisui at an earlier stage maybe before he became good? Unlikely. Could it be danzo? Maybe. Did danzo mix in with the wrong people and do a lot of dirty work? Definetly. So what if danzo has "loaned" shisui's eye to Tobi which shows their connection and how they know each other. Danzo's motive is clear, control over a mizukage and destroying a village from within sounds about right for him. That may of been Madara or even Izuna?
And I don't know if many of you looked into the reasoning for obito but its pretty stupid. His infinite tsukyonomi plan achieves what for him? Create a world with peace and no wars? He was a kid during the only war he'd been in and he didn't even die in that war? I can only see rin as his motive, but why not just target kakashi for that? Acquire immense knowledge and power, try to become like the sage himself, start shinobi wars, kill countless people, massacre clans all for the sake of 1 girl? A little over the top there kishi...
To sum it up, I don't think its plain and simple tobi = obito... If it isn't obito, I sense a pattern... Tobi is Madara, oh wait...hes not? Tobi is Obito! Oh wait...hes not!