I simply prefer the pop-ups, they give full control over reactions on the AI turns. There's no better solution, even the Final Fantasy Gambit system requires an enormous effort to design all the rules to your liking, and you still need to keep switching those rules depending on the encounters. Pop-ups interrupt the action, but do you really want to either give control away and watch your character act without your input or spend time designing reaction rules where instead you could be playing the game?
