Long term this shouldn't be an issue at all. All our systems are currently controlled by our brain - why would next-gen machines be any different in our ability to control them?

A guy I once met was partially blind. He decided to learn how to see again as he was sick of feeling his way around. He took the "evolutionary" option, by starting to walk extremely fast everywhere. For the first few weeks he had a few knocks and bruises as he ran into doors. Gradually he got back his ability to detect objects at high speed.

I think our brain can adapt much better than we realise with the right stimuli :)