I thought and knew it was Obito since he was shown dying under the boulder. Most people will lie though, and say they thought it was Obito but in actuality they believed it was Izuna [More Popular Theory than Obito at one point] or Kagami or Fugaku or Danzou or the Elder Son or Future SAsuke or...
I thought Tobi was Madara because he did a great job in persuading everyone in Narutoverse that he was indeed Madara. Tobi kept telling everyone that he was Madara. Because he was an Uchiha, it makes it look like he's not lying. The masked man himself tamed the Nine tails, knew the secret that the seal for the Nine Tails would weaken during birth, went in and out of the barrier set up by the Leaf without getting notice... who could honestly do all that? Even Minato himself thought that the only person who could do this was Madara.
Kisame also thought this was the case after seeing his actual face. Why didn't he realise it wasn't him? It is because during that time, Tobi's hairstyle looked similar to Madara's one.
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Obviously there were clues that says Tobi might be Obito. Like how his mask only showed his right Sharingan eye... that was quite suspicious. But since I thought there was no way that Obito could survive that boulder incident, and that the episode about Obito was just to show how Kakashi got his sharingan, how he got the scar over his left eye and where he got that quote about rules and regulations from, etc... I thought Tobi was indeed Madara.
The page where he ripped his arm off against fuu & torune was my first major clue (besides the obvious name, hair, & eye). Then what really sealed the deal for me was vs minato, where obito's arm oozed white goo. Regardless if it was his left arm or not, I knew that he was related to zetsu & so I had a simple thought that zetsu saved & trained obito. I was partially right Lol.
