Sega games get a bad rap mostly because its fashionable by people pretending to be knowledgeable. I truly believe that about opinions in general but that's an argument for another day.
Both games are fun, challenging, well designed and constructed. But I give the edge to Goldeneye for theme, sound and intensity.
That's not to take away from Baywatch as it has a great layout and it's own challenges and fun shots. It's just that Baywatch is a little too cheesy and who doesn't love James Bond. Plus I prefer the normal size DMD on Goldeneye.
Full disclosure: Goldeneye is presently a keeper in my collection. And with my short attention span that may change someday. But for now, it rightfully has earned the spot.