1) I´d really lol hard if the theory The Witcher talked about is true...
2) The Crows being a defense mechanism against Itachi´s eyes is possible... but meh, don´t really think that´s it.
I really hope Naruto just trains to be better in his normal form (better chakra control, one handed Rasengan, MORE JUTUS DAMMIT xD) and I hope he improves his Senjutsu limits ( KyuSenjutsu mode anyone? ).
Kakashi getting to be in charge of ROOT isn´t a bad idea, but I think Tsunade would want them reintegrated in her normal ANBU... That´s if she´s up to do her job again... (I mean, from what we´ve seen till now, she´s the "most normal" of the Kages...)