snerd, you're not alone. I have never been happy with the CST trackball.
CST Sin #1: The wedge shape forces you to angle your hand up toward the ceiling (dorsiflexion) which is going to be uncomfortable sooner or later. You could fix the dorsiflexion by adding a palm rest to elevate your palm, except . . .
CST Sin #2: The same wedge shape prevents you from using a palm rest. The thin end of the wedge occupies the space where the palm rest should be.
CST Sin #3: The rollers are a bit sticky. The Kensington Expert Mouse requires less effort to roll the ball, as does the Logitech TrackMan.
CST Sin #4: the buttons are stiff. (Near the top of the CST, they are not so stiff; but down around where your thumb and pinky will be, they are stiff.) The Kensington Expert Mouse has buttons that are easy to click. As does the Logitech TrackMan.
Ultimately I modded my CST, relocating the cord so that I could rotate the device 180 degrees, with the thin end of the wedge pointing away from me. Then you can use software to invert the axes and swap the buttons. This fixes sin #4, because with the device rotated, you are pressing the buttons at the "easy" end, and it fixes sin #2, because now you can add the missing palm rest. Sin #3 remains. Inverting axes and buttons in software is a PITA and might not work in every OS.
My daily drivers are a Kensington Expert Mouse and a Logitech TrackMan. They're better than the CST in every way that matters for ergonomics and usability.