Bourne's stats are better on paper. Trained to be a super soldier and all that. But Martin has way better feats. Frank Martin's action scenes are so over the top they're almost cartoony.
So yeah, judging by screen feats, Martin wins. I don't recall Bourne taking on 20 armed men with him armed only with his polo.
Bourne's fighting style is based more on what a real world fight would be. Frank Martin's fighting is almost like 90's hong kong kung-fu flicks. The fighter with the more outrageous fight scenes win.