Based purely on how much I enjoyed them...
1. Metroid 2
2. Metroid
3. Super Metroid
4-whatever. The rest.
I'm not saying Prime was a terrible game, but I found it virtually unplayable on the Gamecube controller - the aiming was really tanky/sluggish... substantially worse than the Turok games despite having the same dev team.
The Wii port improved the aiming a lot by giving it the IR feature, and IR aiming is damn fun! Although, I didn't like the game because of its design.
First, I found the whole first-person angle removed something from the series. Instead of looking at Samus, all you see is the arm gun giving the game a somewhat empty feel... which was enough to lower my interest.
Second, I found the "scanning visor" feature to be a terribly intrusive to the experience; mostly because the game was constantly forcing the player to switch back and forth "Killed an enemy, gotta switch to the visor and give the whole room an ocular patdown!" - and scanning most items usually ended up with junk text saying something like "Green science goop dropped by a pirate." and that exact same text might be re-used across like 18 different scans. It's not like you could ever skip this process either, because if you did you could block your progress. You end up in the classic needle in a haystack issue where you're wandering the game for hours wondering just what the hell you missed... except WORSE than the 3D Zeldas of the era because you had the whole game to go back through instead of just a dungeon. Some people find this fun, I find it a boring and colossal waste of time!
There was a 2D Metroid on GBA that I thought was a neat idea, but it also came out in a time where Metroidvania was doing essentially the same thing, except better... and to be honest, I was sick of Metroidvania after Circle of the Moon, so an actual Metroid game wasn't really that interesting to me.
As bad as people find the original Metroid game, it released in a time when there was nothing quite like it on the market. I used to keep my codes on graph paper, trade them around to other kids, it was an experience to remember. I played the CRAP out of Metroid 2, hours of it sitting on a hammock between two trees by the water; the fact that there were games like this on Gameboy blew my mind.
When Super Metroid came out, I recognized it was an objectively better game - but at this time I was already hardcore into the RPG import scene; I still enjoyed it, but not nearly as much as the first two. There was a lot of stuff that was WAY cooler in it... but at the same time, it begged for greater story elements - which was becoming a major thing around this time. Maybe if that GBA (or was it DS?) Metroid came out at this time, the story would be different.
Hopefully this clears up anything for anyone who finds that my list is totally fucked =P
I describe myself as a little dose of toxic masculinity.
