This is actually a response to Hamsters question over at CAGDC
First - why not ask the question here? DKF is not limited to DK players by any means and top players on many games frequent this site and would be glad to help. No offense intended to our friend Pigger, but his site isn't all that active... anyway.
I'm primarily a Millipede player and enjoy my trackball games of all kinds. I own Millipede machines but still play other games on MAME with an X-Arcade set up.
For the most part I have few problems with the accuracy and responsiveness. The Pedes play okay but not great, and can be improved by tweaking the trackball settings in MAME. Probably better than using a mouse however you look at it. For Millipede I play at a relatively high level and don't like playing it in MAME at all. For Missile Command, Super Missile Attack, Liberator, Marble Madness, etc it plays fine for me. Sorry, I don't play much Crystal and can't really speak to that. If you are playing at world record level you may detect some differences of course. Also, keep in mind that that balls are different sizes - the X arcade has the 3 inch ball (midi), but Centipede plays with a 2 1/4 ball (mini) and Missile Command plays with a 4 inch ball (maxi). So they will handle differently than the original cabs.
Good luck!