Wild Arms 3's final boss was quite a pain. It had like over 10 different phases, one of them could RESTART THE BATTLE, one needed to be killed only by a full-power summon (which took time you didnt have), and the final form was several different elemental targets. The battle is long and it doesn't tickle.
I wasn't a big fan of some of the bosses in Star Ocean 3 either. Where bosses even on a normal difficulty could be troublesome, the various difficulties made it (for lack of better words) HARD.