Theory On Hooded Man (naruto)
Well I wouldn't be too sure about the whole "eye stitching" thing because think about all of the times when eyes were exchanged during the regular manga, there were no stitches necessary. Madara and all of them kept pulling eyes out and putting them back in like they were quarters in a gumball machine or something. And we do have ample evidence that Shisui Uchiha died when Itachi saw him die; he had already exhausted himself fighting Danzo Shimura and then had both of his eyes ripped out, one unintentionally and another intentionally. But I think there might be some truth to that.
Also, on account of them immediately assuming that it was one of Orochimaru's test subjects, I don't think that Shisui banged anyone. It could be one of those arrangements where it's really not a genetic father-son relationship but more of a teacher-student and he is simply addressed as father.
Then again, if you think about it, who's gonna say no if the creators decide to just say, "Yeah sure there were other Uchihas that survived :P"
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