I love all the Primes, Fusion, and Zero Mission (sadly haven't got around to playing Return of Samus), but Super Metroid really does stand out as the definitive Metroid game. It's the yardstick by which the others are measured.
I honestly don't think there are many long-running franchises with the consistent quality of the Metroid series. Maybe Echoes' difficulty, and Fusion/Corruption's relative linearity could be considered hiccups, but it's a minor complaint over the lifespan of the series.
Wait, nevermind. I forgot about Hunters... utterly passable, but still good for an early DS title.
Other M? I loved Fusion's storytelling. If Team Ninja can deliver an aggressive young Samus (it looks like they took a few of her close-combat moves from Smash Bros!) and keep the other characters interesting without devaluing Samus herself, I'll be amazed, but I'm buying it all the same. I'm very impressed with what I've seen so far.