I knew he was Obito because I started reading the manga in the middle of part 2 before we ever saw Pein. It always bothered me that Kishi wrote the Kakashi Gaiden and then didn't return to it. That mixed with Kakashi getting the MS and Tobi having just one Sharingan in his right eye seemed to scream at me that Tobi was Obito, plus the Kakashi Gaiden didn't seem to fit with the rest of the story unless Tobi was Obito. Simple logic and an understanding of the art of authorship is what convinced me I was right even when most everyone else (this was on One Manga.com) thought he was Madara or Izuna.