That would actually work really well. I kinda love your idea!
Thing is, if I were to make a full game with RPG Maker, I would make it so long that you would get very used to the interface. It would also reach a point where the fights, although increasingly complex and hard, would have much more room for player creativity rather than allowing for 1 or 2 different answers. And you would come very naturally to these solutions due to being very used to the main mechanics.(Which isn't to say there wouldn't be new temporary mechanics unique to each area.)