I wanted to play Metroid again, and having a handheld capable of playing all classic games in one, I wanted to give it a go!
Metroid 1 was done with Zero Mission. I played and beat NES Metroid and can confidently say it’s not my cup of tea. Love Zero Mission and love replaying it.
Metroid 2 was done with AM2R. This was my first time playing and beating AM2R, and a handheld is the right way to play it. Might try to beat the original and the 3DS remake… eventually but it’s not my favorited Metroid.
Super Metroid. I have the snes game, I played it here and… it’s a love hate relationship. I played and beat it before, but not in a long time. And coming off of 2 fusion clones, the controls are way too floaty and watered down for my poor muscle memory. I also got lost… a lot. And it took my 4 hours of game time. About 2 weeks of on and off play time. Ultimately I like it, but this is the oldest I can recommend anyone going back in Metroid.
Metroid Fusion. My personal fav since it was my first game (the save battery died in my original game as a kid and I can beat this game on 2 AA before they die). Snappy fast smooth and I just love this game and replaying again for the untenth time.
Chronologically, it's just after 1, starting right after Samus's escape from Zebes. She doesn't even leave Zebes's star system.
When the other Prime games take place is not clear though. It would be weird to cram all of that before 2 but I don't think there is any other hint pointing at when they could happen compared to the 1-5 series, including Prime 4.
If someone wanted a full main canon run, they'd have to insert that Other game between 3 and 4. Seriously, though, nobody deserves that punishment.