some obvious things we have debated on NB
that Tobi was not obito ( sharingan techniques similar to kakashis)
that the coffin kabuto surmmoned was xyz (tobi's reactions and kabuto's comment made it obvious it was Madara)
that izanagi doesn't required senju dna(so far in the series only danzo and tobi have used it and both of them have senju dna with their sharingan)
that Kakashi killing Rin was a gengetsu (kakashi did it for some unknown reasons atm and tobi should have been able to know if was a gengutsu but it wasn't a gengutsu)
there are many of them and you can add to the list...