I like Deathlike's idea a lot.
Also you say your weapon, armor, and item lists are already final and capped out but you're saying you wouldn't want to remove some of the more or less insignificant many swords and spears for a little more item variety? like bows, axes, et cetera?
also, on the topic of the whole, level 99, HP9999 MP999
To me it's not so much the issue of wanting higher HP or MP values, as it is hitting the HP, MP, and Level caps before I'm done with the game and before my stats max out.
A simple solution would be to lower HP and MP values so they are worth more so you don't have to have as much.
To solve the level cap you could increase the level cap to 256 but then make levels happen more frequently and have less gain so it's more of a gradual process and you are designed to not hit the caps of things on a regular play through.
This way the player doesn't feel limited to 9999 health, not only that but this way things that allow you to have a certain percentage more health wouldn't be artificially capped, and also your weapons will always do their full damage and not have the damage capped. This would more realistically seprate and show how much better some weapons really are rather than having all the best weapons do the same amount of damage.
I understand it would take a lot of value releveling and rebalancing but I think it'd be worth it to have no artificial limits in the game, and so that the weapons would have more diversity in the damage they do at the end of your game.