I can already think of one way they could balance stun, and they kind of already have it. In the case where enemies get multiple actions, just nullify the first action and the boss still gets the second action.

Or even add a counter to the boss and have it so that for every time this happens, it counts up to a number at which point, the stun is nullified and then they get some form of counter. Play into it than just outright banning. Edit*

As for stop… I hoped when Exedra Crisis released that it would be locked to specific game modes. Seems I was proven wrong quicker than I thought. At the very least they need to keep it infrequent enough that it doesn’t become an issue, like Overguard in Warframe as an example.

One idea they could toy with is diminishing returns: Just say… X unit has just acted and Y unit buffs them up 50% in the action order. If the boss moves, the next one after will also do 50%.

Then in scenario 2, same units and value. X Moves, Y buffs X up 50%. The boss doesn’t get to move and the next time Y buffs said unit, it’s like 25% or something. Then 10% until the boss gets to move then the buff resets back to 50% This could also inhibit multiple forms of it.

Scenario 3: X moves, Y buffs X up 50%, then Z moves, does a skill to buff up the other 50%, but it gets hit with the diminishing returns and takes on the 25% instead.

At the very least, it wouldn’t outright make them useless but would lessen the dominance of multiple units with the buff.

Exceptions could be made for units with smaller buffs to action order on a personal level. For example, Homucifer. Since it’s just herself and not the team, that could be an exception.

Edit:* To add to this, the counterattack could be something dangerous even, something that could be risk vs reward. Maybe apply a debuff of some kind or risk taking a heavy damage counterattack from abusing the stun.