With the Rinnegan Tobi, the Biiju will probably be part of an ult and he will have other things for combo's and jutsu. Biiju Naruto will be similar.
As far as Susano'o Sasuke, they balanced his high attack speed with the "hard-to-land" ultimate and the very linear jutsu. Kyuubi Naruto was balanced with the face that he has to awaken, and if you survive he has PAS (Post Awakening Syndrome) and is at a disadvantage. Plus, his combos are almost unchanged from 9-tails rasengan Naruto.
Yes there will be more op characters in the game. But they will attemp to balance them. Unfortunately, they balanced some of the less op characters too much. *cough...Tenten, Tsunade, Temari