Well to combat imbalance in team selection, ninjas can be given tier allocation.

Example:
Tier 1: base Ninjas like lee, hinata, etc.
Tier 2: Breakthrough base Ninjas like BT Lee, BT Sasuke, etc.
Tier 3: Mid Tier Ninjas like Masked Man, Jonin Minato
Tier 4: God Tier Ninjas like sosp Naruto, 10 Tails Obito, etc.

So the way around this is to make each team be the same level. Meaning the tier level of each team should be the same.
Example: Jonin Minato, BT Lee, Sasuke (3+2+1= 6) vs sosp Naruto, hinata, sasuke (4+1+1=6)

Now the tier system should use a little bit more work because honestly I'm to lazy to comprise a huge tier list to satisfy this game mode, but this is simply just a suggestion for the system the player is trying to push. And there is still a problem of team composition, as even if the level of the teams are the same, some teams work far better than others (which in turn pushes us back to the start of unfair balancing). So, in my opinion, it is a good idea, once you can solve this issue of unfair balancing, as if its there, its just going to be an annoying system that most won't do.

Nvm just realized I just said what Zenith is :/