Game has the same kind of quests. Fetch herbs but you just haphazardly mow over most of them. Save a farm from bandits except you're just blasting them. Kill quest to take out some liches tower but you just blow it up instead of raiding it.
All the npcs treat you like you're not a tank and are baffled by the way you complete their quests. Maybe get really absurd by completing some kind of mount upgrade where you're just a tank on top of some huge horse and it doesn't really make you any more mobile than before.
Another option -- which is good for being busted to begin with -- is lateral progression. I should have explained myself better, but part of the reason I mentioned ammo types is because it would let the player potentially doing things differently rather than strictly better. For example, maybe you have a finite number of special shells you can take with you on a given mission, but you can unlock more types of shells that you can take so it becomes a question of which you want for the mission.
Incidentally this all reminds me of one of the incredibly dumb things that I sometimes kick around in my head: What a serious One Punch Man mod in Skyrim would look like, specifically one where you play as Saitama but the game is superficially the same otherwise. Most of it is just figuring out how to give alternate explanations or adequate circumventions for the necessary set pieces, and how to control a character that theoretically should be able to run well beyond the speed of sound and jump to the moon.
The primary way the one punch author skirts around the issue of having an infinitely powerful character is by having the power levels of the characters around him all adhere to the same tropes of shonen manga/anime, and mainly wheeling out Saitama to deal with the main baddies. Actually I've only read one punch sort of cursory but that's what I took away from it. So I imagine it would have to work the same way in this game, and otherwise yeah you'd have to have some kind of difficulty that relys on lateral solutions rather than the absurd brute force you have.
Which, honestly, is where the best written shonen tends to land on. Good authors can make powerful characters and either neutralize them in a believable way or put them in situations where being stupid strong isn't going to necessarily solve everything.