He can't sustain KM for very long before he has to come out of it to allow for a rest and reset. He can't stay in SM too long as he can't continuously draw natural energy while moving less he turns into a toad statue. His chakra how ever is not being used when he is in either mode so when he runs out of the other two options, he still had the capacity to fight at his full base power. Well, at least that's how I see it.
I understand that some may see it as unfair to fight him, but what about the unfairness of the Uchiha? When the EMS starts to become bs for them, Kishi will give them some new level to the eye and Sasuke will be completely overpowered compared to everyone else. What I want to see is Naruto combine the Sage and Kyuubi mode and become the Sage of the Nine Tails.