You can replace the thumb-pad with one from a normal Turbopad/PCE pad. They are raised a tad higher so your thumb doesn't sink into the circular pit surrounding the thumb pad and grind on anything. It is an easy swap out. In general the plastic on those TG/PCE thumbpads feels better/smoother, so I recommend swapping them out.
I actually replaced the d-pad in mine with one from a third party Genesis pad. It works a lot better, but if I'm doing six button games I still stick with the Hori commander.