Out of the 2D metroids, I think Super Metroid still takes the cake. Dread and 2r are still pretty good but there is a reason why super metroid game design gets taught in college game design courses. One of the best games of all time probably, still trades blows even with good modern metroidvanias. I played it for the first on in the Wii back when I was in high school so this isn't even nostalgia talking, I even played it after the Prime games.

For the 3d ones, both Prime and Prime 2 are classics imo. Just the sheer immersion is something you don't find too often in video games. Prime 2 gets a lot of flak for the ammo system and dark world constant damage, but I think those were useful improvements to balance the game since Prime 1 is quite an easy game. They do add a decent amount of friction to traversing the world and makes the dark world feel actually dangerous to be in. Prime 3 was a bit more forgettable but still not a bad game.