The best thing about the BoF series was the loose continuity the first three games seemed to share. In my experience with RPGs, that's fairly unique. Especially for a JRPG. Western titles seem to like making direct or relatively direct sequels, but it wasn't really until Xenosaga came out that a game series would actually have any continuity.
I mean, yeah, around 2000 you had Chrono Cross and Megaman Legends 2, and LoZ started embracing the idea that there was continuity and time-lines after Oranica of Time, but BoF was a real pioneer, making direct references previous titles, even with recurring characters that weren't merely easter eggs invoked with temporal or dimensional silliness.
Take Blue/Deis as an example; she literally slept between games. Far as I know, that's pretty unique for a recurring character.