I've always found the esper level-up bonuses for HP and MP to be a total waste. Your characters are so close to 9999 HP and 999 MP at level 99 there's no real reason. Plus, with things like Green Berets, Red Caps, Crystal Orbs and Muscle Belts it's easy to augment your HP and MP if you're deficient in one or both or you need more. The other stats are harder to come by and seem to be much more useful in the long run.

Thus, I deem that the HP and MP level-up bonuses are for impatient people and they should learn some patience.