I always liked how that worked with Sephy gaining more HP. I also heard he is significantly stronger if you are lv99, though I don't know how true this is.

It would be nice if they made last bosses with 'I just went right through and beat the game' difficulty and 'I got everything' difficulty. It would really lessen the need for extra uber bosses in the game if they could just find a way to have the last boss scale intelligently. (Using triggers for every extra event you clear or something)

Then again in the earlier games it was almost assumed that you collected everything in order to beat the game at all