I would incorporate something like Hades Heat System into the game for optional challenge.
Here's a picture to demonstrate what it is for those that haven't played Hades (Don't mind Northernlion in the top right corner).
These are individual modifiers that you can toggle to make things trickier, in Hades it does stuff like have enemies have more HP, you start with less HP, give mid bosses extra attacks, put on a time limit on how long you have to beat each area and so on and so forth.
You can have a pokemon equivalent of stuff like Opponent trainer's pokemon are 5 levels higher, give them more healing items to use in battle, each pokemon has at least a perfect IV per level, maybe have an extra pokemon, gain less EXP or Money on victory. Stuff like that. Turn on whatever difficulties are to your liking. You can even include the "Battle Style Set" into the system like this already.
Now in Hades you get the reward of Diamond, Ambrosia and Titans Blood for defeating the bosses at set levels. For Pokemon, I can see an equivalent of being to give players BP for battles. That way when they get to the BP Stores in the post-game (Or mid-game with a select assortment of items that wouldn't break the game at that specific time) challenging themselves earlier gives them rewards on their post-game progression and team building. If not BP, an equivalent currency could work (But we have like 3 of them now, don't want to have too many currencies.)
You can also do the inverse and have a Celeste like assist mode in the process to make things easier too for those that want it. Options aren't a bad thing to have.
