Ya the fact that Madara fought the forth is solid proof against this theory considering Tobi was fully grown during that fight and Shisui would still have been a kid at the time. But for me, the biggest plot hole is that Itachi referred to Tobi as Madara. Wouldn't he have known it was Shisui if it really was? I mean yes Itachi lied to Sasuke a lot, but he never lied to him in regard to Madara. He was always very forward and blunt about Madara's hatred and his malevolence, I really doubt he was shisui for this reason.