"Somehow, at the last second, he transfered all his eye techniques into you", says the very shadowy and mysterious Tobi/"Madara". Hell, I wouldn't be surprised if he wasn't the real Madara anyway, but maybe his eyes are and we all know how strong forces like Orochimaru seem to try to take over the hosts. I still have a gut feeling that Tobi/"Madara" actually implanted Itachi's eyes on him w/out his consent.
Or maybe that is what I would prefer to have happened anyway.
EDIT: I sometimes even think that whole Itachi monologue by Tobi was a load of crap. Probably some genjutsu with all those sharingan shots of his. Sasuke suddenly remembered Itachi crying after killing everyone, after the little chit-chat? I don't buy it. Same with the recent Naruto chat. Both dumbly looked straight at him and what's to prevent Tobi from doing "something"?