After experimenting for many years with many kinds of mice, trackballs, touchpads, trackpoints etc. in the search for the most comfortable graphic pointing device, I have settled to use, instead of a mouse, a small Wacom Intuos graphic tablet (usually with Linux), configured in its "mouse" mode, i.e. with relative coordinates, not with its default absolute coordinates. At least for me, using a stylus has proven to be…
What kind of usage do you do with your pointer? I find that with code editing, it's annoying to pick up / put down the stylus all the time. Have you tried a vertical mouse? That is the best for me: comfortable, yet mouse-y :)
This allows much faster transitions between typing and pointing than with a mouse.
I have not tried a vertical mouse, but I agree that it is likely to solve most of the comfort problems caused by a classic mouse.
Nevertheless, there is no chance for it to be as fast and accurate as a pen. With the pen I can point to any place on the screen pretty much instantaneously and using a negligible muscular force, due to its lightness.