[Contains 2D Metroid Spoilers]
Zero Mission is my favorite game in the series, sure Super and Fusion are great, but Samus' control is so responsive, fluid and tight in this game she's a joy to control. If you see the 3D games as a separate category of Metroid, I'd say Prime 2 is my favorite. IMO the difference between Prime 1 and 2 is purely aesthetic taste, which environment do you prefer? I realize some people were off-put by the light/dark mechanics, I was too initially, but they no longer bother me at all. I felt Prime 3 was a little weak and didn't care for the inclusion of voice acting. I did love the improvements of play control though, I really want to play through 1 and 2 with the Wii controls, so I can actually aim while moving. I am not a fan of lock-on targeting.
In terms of story Fusion is my favorite, it feels like a legitimate sci-fi thriller, I love the mystery of the computer identity, the origin and threat of the SA-X, the threat to Samus from the Federation, and most of all the idea that Samus is now part Metroid in order to save her life. The story of Super Metroid is lauded, mostly for the moment when the infant Metroid returns to save your life. Nothing against it, but it's also pretty simple, you saved it's life, it returns the favor. Story-wise I was a little let down by the whole idea that you're revisiting the same base from the original game, second Death Star anyone? It was cool that the Metroid imprinted Samus' as its mother in Metroid 2, but wouldn't it have been cooler if Samus kept it as a personal pet instead of giving it to the Federation? Still, I do really like that the Metroid DNA saved Samus in Fusion, that's awesome.
Prime 1 has a great backstory, but if you're not reading up on it, the present is pretty straightforward. Prime 2 is essentially the same story, except that there are living survivors, and I think the idea of two worlds in and out of phase with each other is quite cool and dramatic. Prime 3 tried to do religion vs. science, but I don't think that was explored in a way that was interesting, it was a pretty tired cliche if you ask me. I never played anything on the DS or after Corruption.
Edited by Cukeman, 02 July 2017 - 03:29 AM.