Something I've seen from speaking with a lot of people with overuse injuries is that what activates a person's injury tends to vary a lot. I'd heard elsewhere that touchscreens were terrible and didn't try them for quite a while as a result. But for me they ended up being better for a lot of things. Additionally, game controllers are a large improvement in my case simply because I can hold it in my lap instead of extending my arms, and in my case there is only limited finger pain (more arms, elbows, wrists).
The ideal here, however: are motion sensors--like the Kinect, but better. In fact I started out working with the Kinect, but it's not precise enough imo to create a nicely ergonomic coding system. However, things like The Leap (https://www.leapmotion.com/) may be: it could take very subtle cues as inputs and track light hand motion.