I haven't used a mouse in about 5 years now, and I'm not sure I'd be able to go back! My set-up is a Wacom Bamboo graphics tablet perched on a writing slope, so my desk space is now mostly sloping rather than flat. I recently upgraded my graphics tablet to the 'pen and touch', assuming that I'd use the pen a lot less, but actually using your finger instead for fine control stuff isn't all that intuitive or easy so I find myself still using the pen a lot. That said, the gestural stuff is pretty useful, so I tend to switch between the two, and use gestures for broad-brush stuff like scrolling, and the stylus for more controlled stuff.
All that said, I recently discovered that my problem was in my neck, not in my wrists at all (despite a diagnosis of RSI years aback), so my biggest challenge now is postural and keeping my neck muscles loose and unknotted. Easier said than done!