An interesting idea. I imagine combining it with classic spell casting system, but using this physics based 'marble drop' to determine the outcome of the spell rather than the simple (and invisible) probability.
I'm not sure about the use of the drag and drop for the marbles, since I want to look at the main game area and the incoming slots for the marbles at the same time. Perhaps there's a way using the keyboard to select the ball and slot, though I suppose this wouldn't work for mobile platforms.