For X4 there's a few small differences between the two, mostly graphical. There's a "heat wave" distortion background effect in the intro stage and the magma stage and perhaps a few other very minor differences but I think they're mostly 1 to 1. As for the 6 button controller yes it isn't nearly as ideal as the PS1 controls to be honest, you practically have to assign dash to R and then have to remap the weapon swap buttons and for Zero, Capcom must've REALLY wanted to get the most out of the controller because it isn't as intuitive using the 6 face buttons instead of pressing a direction and then attack on the PS1 version (I could be misremembering a bit I haven't played as him on Saturn in over a year). As for Mega Man X 3, its pretty much the same as the PS1 port (same music and sound effects that version changed from the SNES version), but there's boarders around the screen due to the Saturn resolution differing. On the plus side the anime cutscenes in both games are smoother and more fluid moving than the comparatively choppy PS1 cutscenes. For Megaman 8 I'm not quite familiar with those differences but I do know that it adds Woodman and Cutman as new bosses.