Well, I have had similar problems due mostly to sweat. The bumps on the stick work to prevent this, but aren't all that great at it.
You might want to try something like rubber cement. Once it dries it should be relatively rough, and will slowly wear down to be even.
Alternatively if you really like the xbox stick, you could cannibalize one and swap out the tops. OR you could look for those little rubber slips-ons they sell as replacement or improved caps for xbox or playstation controllers. If the sizes are similar, then they might fit.
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