I think the following would completely fix the battle regimen system:

When someone stacks an ability on the BR queue make it so the stamina required for that ability is 'set aside' or grayed out so it is unusable. Allow the people who have stacked abilities to continue to fight normally while their ability is stacked except they just have to use a smaller stamina bar. Once the BR activates the player is given back the 'set aside' stamina and they regain their full stamina bar. This allows BR's to not break the flow of battle.

The other thing that needs to be fixed is the glitch where the BR's wont activate and you have to go passive in order to quit out of it.