Ee's in charge because of several factors. Since Nagato's attack, Konoha's defense has greatly weaken. Kumo has the greatest military strength and control of a Jinchuuriki. And finally, Tsunade's record in a battle isn't all that great. Even though she was suppose to be protecting Naruto from getting caught by Akatsuki, She instead sends him into a fight he would have lost. Trust her with both Jinchuuriki and this war will end up being over quickly.Why is the Raikage in chrge of everything but now since tsunades back we can acually see how good she is because shes only fought Oorochimaru and she was pretty good there but she is hokage now.