A thing I've come to feel is a shortcoming of the metroidvania genre is that the mobility-upgrade-based progression often finds itself in uncomfortable tension with the puzzle-platforming gameplay that stands as one of the genre's central pillars. The interplay between the two typically leads to a situation where the early game's platforming puzzles have little variety because you've got so little to work with, and conversely, upgrades obtained in the late game go badly underutilised outside of the optional map cleanup phase (which, if we're being honest, most players don't bother with anyway).
What I'd love to see is a metroidvania that addresses this by bridging the gap between Super Metroid and Super Mario World and tightly coupling its upgrade scheme to ability-granting pickups. That is, you can encounter literally any ability in any part of the map, in the form of a temporary pickup that lasts for just that one puzzle. Maybe there are force fields you have to pass through that remove all of your temporary powerups, preventing them from being taken into other parts of the map, or maybe there's some other limiting factor. Permanent upgrades would then take the form of being able to toggle specific powerups at will, without needing a pickup, enabling them to be brought into "unintended" parts of the map.
Heck, if you want to get excessively clever about it, maybe there are situations were picking up a certain powerup is unavoidable, and you need the permanent upgrade that lets you toggle that powerup at will in order not to have it active, which is beneficial in that situation for some goofy reason. Or maybe there are cases where the powerup-removing force fields along a certain route are themselves avoidable using some non-obvious trick, allowing powerups encountered along that route to be smuggled into screens where they're not normally obtainable prior to gaining the ability to toggle them.
Like, imagine the speedrun routing.
(Also, for bonus points, it should cut directly against the customary underutilisation of late-game upgrades by having the very last powerup you gain the ability to toggle at will present as a mandatory pickup for solving the game's very first platforming puzzle.)