I think he might have KA, because I can't think of how else he controlled Yagura with his MS when Sasuke couldn't even use a genjutsu on Bee with his MS (maybe Sasuke sucks at MS genjutsus?). And also Mei speculated that the jutsu Tobi used on Yagura was the same jutsu Danzo used on Mifune, and Kisame confirmed that the Tobi that controlled Yagura was the same one he met in the present time, who happened to be Obito....