The Gen X has some minor audio issues, but a more solid on-screen display (none of the odd "rolling" between screens like the FC3)
The Gen X controllers are MUCH more like the Genesis 6-button controllers.
The FC3 appears to have better audio, no noticeable sound drop out, but a strange "rolling" on screen in areas where the game doesn't display any on-screen data. VERY hard to explain, but reminiscent of the way old analog cable tuners/boxes would distort for a millisecond when changing channels.
I don't think one necessarily outweighs the other in terms of "quality" and both have the region switch.
I think it's really up to you from there.