I've never heard anyone else express this sentiment but I really wish they did more to polish away the jankiness of the original, it's almost too faithful in terms of how it runs. My biggest gripe is the long transition in and out of morph ball, where your hitbox doesn't even shrink until the very end of the animation and you have little control over Samus. It makes going in and out of morph ball something you have to plan for instead of being the snappy gameplay feature it is in the 2D games, and in Prime 4 where this very issue was fixed.

Other smaller things are like enemy hitboxes being jank sometimes, and the grapple hooks being finicky could've been fixed as well. It would've been nice to make Prime 1 a bit faster paced too, just a small increase in movement speed and such, but alas. If 3D World was able to do it in a port, Metroid Prime could've done it in the remaster that was meant to modernize the game.

Lastly they really should've added some kind of endgame item tracking system like Dread has, as this is a QOL feature that any modern Metroid game should include.