But certain ninjas are semi critical to certain mains, which means if they are banned, then the optimal setup would require a main change. Forcing someone to do a main change is... just horrible.
Just think, how many people would use water main if sailor sakura is banned? Or, god forbid, sailor sakura AND mei. There are VERY few water main who uses neither of those.

Also, some ninjas are rather exclusive and an advantage people paid money for. Banning those isn't exactly fair.

Things would certainly be interesting if every battle come with an "arena quest" for both side and they must meet the requirement of that quest. (quest will change regardless of win or lose between each round)
Thou... if there is going to be RNG, best 2 out of 3 probably isn't enough, as it leaves too much up to chance. 3 out of 5 or 4 out of 7 might work thou.