Having thought about this lightly before, I'd say choose whatever works best for your story. I'd lean toward natural aptitude, though, since it allows the speedrunner to explain their choices and makes them less overpowered. Letting them always know the best solution might harm suspense.

I would advise you to immerse yourself in the subject! Pick up a game (doesn't have to be a long one) and give it a spin, spend a few hours experiencing it yourself and it might provide some natural insight.