Weren't the final bosses in FF's not that challenging by design? I have the distinct impression of reading something about it, that the final bosses were never meant to be too hard, but to be as a step up from the previous ones, while having the hardcore boss hidden somewhere in the game, for the one who wants a real challenge.
Oh yeah, the idea of super hard hidden bosses is one of the best things in Final Fantasies. I don't think I've ever beaten one (unless you count the flying and underwater Weapons in FF7 as one of them; I never beat the desert boss though). I've found the hidden bosses in FF5, FF7, FF8 and FF9. If I found one in FF4 or 6, I don't remember them.
These hidden bosses give a nice sense of an additional mystery to the games. They are never really explained so they leave this nice feeling of "so there is this kind of a creature/entity in this world minding it's own business somewhere out of the eyes of the regular people." It gives the player a new thing to use to create the world in one's own head.