A cool idea for an endgame item here. An HM card/orb/whatever (item doesn't matter). Basically, this could be crafted and used on a pokemon to bind a power to it. The power would depend on the pokemon.
Any pokemon that can use cut would make it able to cut down trees instantly, like in the treecapitator mod.
Pokemon that can use teleport make it into an infinite ender pearl.
Pokemon that can use flash make it create a light around the player when held.
Pokemon that can use strength make it apply several temporary buffs to the player when used.
Ones that can use rock smash make it create a tnt-type blast that destroys blocks.
If it can use dive, it applies a long-lasting waterbreathing buff.
These are just what I could come up with off the top of my head. Doesn't need to be specifically these, some should probably be nerfed.
TLDR: a special item that would add several new abilities and buffs based on HMs and their uses in the core games