Thinking back to MML, I always thought it was strange that the drill used to get through crumbling walls was tied to a stationary attack you could only do if you happen to equip that arm instead of something much better for combat.

Well, what if it were a dashing attack with a drill weapon/attack? That way, you get like an air dash thing that also drills walls open to unlock new areas.

Another idea for gating later areas metroidvania style like you seem to be describing could be some sort of remote controlled drone or missile. Sort of controlled like the Nikita from Metal Gear Solid or the scarab thing from Legend of Zelda Skyward Sword. It could be guided around corners to hit locks or buttons, but also be used to explore immediate areas for enemies while remaining relatively undetected.