In my opinion, a finger-ball is a better choice than a thumb-ball, because your fingers have greater dexterity and range of movement than your thumb. Plus you can switch fingers on a finger-ball (I use my index, middle and ring finger to manipulate mine) to avoid fatigue when you shift hand position. You wouldn't sit with your legs crossed the same way for hours on end, why would you want to maintain the same hand position for that long?
IMO, the key to long-term comfort is to change positions periodically. Having a ball or mouse that doesn't mold right to your hand will allow you to do this without compromising comfort. Most thumb-balls force you to maintain a particular position in order to use them.
I'm sure a lot of people will disagree with me on this, but it's my story and I'm stickin' to it.
Anyway, I used a Logitech Marble Mouse for several years, great little trackball but it has no scroll wheel and the two little buttons are useless, so for my applications it was a 2-button mouse. The thing that finally killed it for me though is when I upgraded to an HD monitor and noticed the lack of precision.
The L-TracX which I use now is an excellent mouse, very easy to modify with a little soldering experience. With that said, there was definitely a break-in period, both for the ball to smooth out and for me to learn to use it precisely. The first few times I used it for long periods, my hand actually felt worn-out a bit afterwards, I assume this was because I was using different muscles than I was used to. Now I have no problems with the 'ball, I find it very precise and very comfortable.
Just my thoughts, hope it helps!
CZI