You have to get through the first 10 hours or so of plot in BoF 1/2 before they start getting interesting. Up till that point they are fairly generic fantasy RPGs, but past that point you really get to the central plot in 2 revolving around the crazy evil God and his pseudo-catholic church and their machiavellian plots to destroy diversity and individual will and it gets pretty epic. Similar thing for #1 with the light/dark dragon clans and all that.
In contrast I found BoF3 kind of banal, the music was this terrible jazz muzak crap, the setting was cool in concept but in practice it meant you spent 99% of the time in this tiny little generic fantasy island (except of course the furry races were 100 times cooler than elves and dwarves) and then 1% in a couple cool Planet of the Apes "you blew it all up!" kind of scenarios and then you face down the Goddess who is basically a watered down feminine anti-gaia take on the deity figure in the second game. Actually I thought Wild Arms did the anachronistic/post-apoc desert wasteland kind of thing way better.
As critical as that sounds, I did actually like BoF3, just not enough to ever play it again. I never played 4, didn't own a Playstation at the time and haven't got to it since.
@Lumi: in BoF1 you really had to dig to get at any backstory or personality with many of the characters, but you have to understand that the fact they HAD stories is way more than most RPGs of the era had so it was really innovative. Another big thing was it was one of the first console RPGs to break out of the Tolkien box and develop a unique and interesting setting. BoF2 really nailed the whole religion/deity plot thing down better than most other games have to date, too, and it made for some great fiction. Also, the gameplay was just plain fun. It was one of the first RPGs to have animated players and monsters, and yeah the transformation thing was pretty unique.
Oh yeah they were also one of the first games to include minigame diversions (outside the casino in I think it was DQ4), which for me was a slippery slope as by the time you get to FF7 you actually are FORCED to play gay little minigames in order to advance the plot, but whatever.