Honestly, I think a lot of games have surpassed (the 2D) Metroid games, especially in terms of control and gameplay.
I can't think of a single 2D Metroid game that I actually enjoy specifically for the combat. That aspect has always felt serviceable at best, clunky most of the time, and at worst actively irritating (like Samus Returns for me, didn't like the parry mechanic at all, felt so overused even in the short time I played it).
I actually appreciate the leveling and weapon upgrade mechanics in the more "Vania" style games because it actually gives me a reason to engage with fighting enemies and not just skip them whenever I can like in 2D Metroid games. Especially the DS Castlevania's where you get abilities as random drops that give you all new combat abilities/spells (whatever they were called).
And I've never played a Metroidvania with leveling mechanics that I broke the balance unless I was ACTIVELY trying to by grinding for levels, and it's not like in Metroid games you can find most of the the missile and health upgrades (don't even need all of them) and be basically unkillable by the end.
It doesn't take away from the permanent upgrades at all IMO since those are still needed to traverse and explore the world.
I can't agree at all. Samus Returns IMO is worse than many small indie games. The combat changes are unnecessary and break the flow of exploration. Stopping to counter enemies every few seconds is not Inter gameplay. The level design is very poor for a Metroid game, and the incentives for exploration are weak. I know seeing a not terrible Metroid game after a decade of silence and Other M and MPFF really threw people for a loop but that game does not stand with the rest of the franchise. And I don't even love Hollow Knight as much as many people seem to.
Yeah, I only played Samus Returns for a few hours before dropping it. The first Metroid game I've ever done that with.
The fan made AM2R was the superior Metroid 2 remake IMO. I probably would have finished SR had I not played it after AM2R, but it just felt inferior to me in every way (didn't like the look of it or how the combat felt).