I actually prefer the new music...but maybe that's just because I grew up with the PC version. I also have the Mega Man X Collection on PlayStation 2. I've played through a PC version a million times. I love it. Hah. I can't remember if I bothered to play through the PlayStation 2 version, since I had already beaten it on PC so many times. I think I played it for a bit, though, and didn't notice any differences. I also watched my younger brother play through all of it, and it seemed the same.
I'm not really sure what makes the SNES version "better." I think the other versions are fine. I haven't played the original much, though. Anyway, if you do go for the original, get the Super Famicom version, as it's WAYYYYYY cheaper than the U.S. release.