Its Super Metroid for me. I like pretty much every Metroid game (Other M and Hunters not as much) but Super Metroid is one of the few games that I consider to be perfect. To me everything about it just seems great from start to finish.
Prime 2 has plenty of flaws but it is still my favorite of the ones I've played. The Dark Samus fights were really great, the Luminoth were cool and it is nice to see an actual living alien race in Metroid and it had some really nice boss fights and concepts (Caretaker Class Drone is really cool despite being a miniboss). Heck, what other games in the series had you fight bosses entirely in morph ball?
Prime 2, my introduction to the Metroid series. Loved the challenge, the atmosphere, the awesome stand-offs with Dark Samus, the Luminoth, the ammo system (yes indeed) among other things. Of course, it is not a perfect game, but for me it is the definitive Metroid experience.