The idea seems really great, but this prototype is a little lacking in gameplay. As you said, this mechanic is meant to link together the story and the gameplay, but atm it feels like an interactive menu...
I liked how the choices that would be the most difficult were higher, thus making you jump higher for them, but at the same time, pushing a button for half a second longer doesn't really have the effect it could as opposed to there beeing different paths on which the player could go and the ones for the more difficult questions would be harder to traverse...
Anyhow, it'll be quite interesting to see this implemented in a more complete game.