@meleu :)
fbalpha is a maintained core (it has a number of programmers working on it) whereas mame2003 is basically mame exactly as it was in 2003, as far as emulation goes.
fbalpha is also used in the fighting game community (i think it's the core of that online thing that was/is quite popular), so i would guess that most of the popular fighting games are running pretty much perfectly.
so on that basis, i assume that fbalpha is the better one.. but that said, i use mame2003 for every 2d fighter it can do, and i've not noticed anything much, other than it not supporting certain rom hacks that fbalpha does. if i could wave a wand that would swap them all over for me i would probably do that, but it sounds a lot of hassle :)