My favorite 2D entry is a ping-pong match between
Zero Mission and
Dread. Story-wise... I just really like whenever we get insight into Samus and her relationship with the Chozo. I like the brief monologue at the beginning of
Zero Mission, where she reveals that Zebes used to be a peaceful place that she called home before the Space Pirates set up shop. I like the epilogue where it turns out that the Space Pirate compound you've been sneaking through is not only a renovated Chozo Temple, but the same one that Samus was raised in. There's a little drawing etched into the wall. Like, look at this cuteness.
And
Dread. The reveal trailer already had me hyped, but learning that we'd be meeting a Chozo? HELL. YES. Getting to actually see Samus interact with some outside of a flashback was awesome, and I was just as pissed as Samus when Quiet Robe got shot at the end of that cutscene. Oh, and getting to hear Samus speak Chozo? Absolutely made my day. Give me more of that. Have Samus quietly mumble in Chozo to herself when left idle for too long, I dunno, just give me more. And the only note I have for the big "I am your father" reveal cutscene is that her real dads are hidden in shadow and that bums me out. So yeah, I like Chozo stuff, and those two entries gave me a lot of it.
And gameplay-wise... they're just really, really great.
Dread has the best boss fights in the series, but to hone in on similarities again,
Zero Mission and
Dread have a nice balance of being structured enough to guide first-time players and allowing veterans to leave the critical path to sequence break. I understand the critique that it feels like the game doesn't let you explore on your first time, and that it can feel like a guided tour, but... I dunno. I never had a problem with it. I still had the freedom to leave the critical path to do early Varia in
Zero Mission the first time I played that, simply because I noticed I could bomb jump infinitely and was curious if I can time my way past some enemies to climb up all the various shafts in Brinstar. Or early Gravity the first time I played
Dread, because I was stubborn about getting to a teleporter I saw, then became even more stubborn about getting to the end of a Shinespark puzzle. I still don't know when you're intended to actually get it. And part of the beauty of 2D
Metroid is its replayability, where you can go back in and experiment with the knowledge you gained on previous playthroughs. It doesn't matter to me how "as Nintendo intended" my first playthrough might be, because I'm immediately going back in on Hard Mode thinking "okay, now that I know that [X] is there, I wonder if I can do [Y] or [Z] to reach it early?" Plus, since I started playing
Metroid with the GBA, the movement of those games resonate with me more than
Super; I actually never beat
Super until 2021 actually, because I had never fully invested into
Super's game feel. I totally enjoy
Super now and have beat it a few times, but I still like the movement of the GBA and MercurySteam titles far more.
It's been too long since I've played
Echoes or Corruption, so I'll get back to you on my favorite
Prime whenever I get around to replaying those.