Super
Prime
Zero Mission
Prime 2
Returns
Fusion
Metroid II
Prime 3
Metroid
Hunters
Other M
Super Metroid was my favorite game for the longest time, until i played Earthbound, but I think just based on game design alone it's still one of the best games ever made, and visually it also holds up extremely well. Prime is almost just as good, it blew my mind when I first played it, so it only loses out by a hair.
Every game from Zero Mission and down to Metroid II are also great games that I regularly replay, and some I even speedrun. It's very difficult for me to choose between Fusion and Returns, will probably have to play Returns a couple more times to really make up my mind.
Prime 3 is the first game on the list that I think is just decent at best and that I don't really think I'll replay in a long time, it had so many issues. Metroid I highly respect for its impact, but it hasn't aged well at all. Hunters plays absolutely awfully and its story mode is a joke. Other M might actually be a better game than Hunters gameplay-wise (not saying much though), but then there's the story and 'sending the series on a 7-year hiatus' part which I don't appreciate.
Not ranking Prime Pinball because there's no point in comparing such different genres, and unlike the other games I didn't actually complete it. I never bought Federation Force. AM2R would fit in just below Returns.