At the end it would be EMS + KM Sasuke vs 3 tomoe + BM Naruto. Which I guess is somehow balanced, since EMS is a lot stronger than just 3 tomoe, but also is BM a lot stronger than KM, and Naruto would probably still get SM.
With only tomoe Sharingan most Sasuke would be able to do is supress kyuubi to not take over.
With MS/EMS could possibly control it at times and even get KM, but he doesn't have KA so he can't keep kyuubi under genjutsu forever.
For BM you need cooperation, and by taking control of him, Sasuke would only enrage the kyuubi even more, cause kyuubi would feel used, etc.
Naruto could possible unlock MS by the dead of someone like Jiraya, but he'd be better off not using it, to not go blind lol.