MP1
MP > MP3 > MP2.
IMO.
As I've said about 2939249 times before. >_>
^All of this. MP was a 3-D metroid, through and through; you take Super Metroid, change the perspective and build a new adventure around that basic gameplay and you get MP. Everything good about the series is exemplified in this game.
MP3 was awesome; the controls, the gameplay, the graphics and mostly the tone. It's problem was that it was moderately short and the story was your quintessential sci-fi action fare. It was a decent story, but overall that level of immersion from MP wasn't there due to the more action based gaemplay coupled with dialogue.
MP2, I haven't played all the way through, so I won't comment on. I will say that what I played was fine, but the whole Dark/Light thing bothered me, and not because it was cliche, but because it seemed more like magic than sci-fi, two things I hate when mixed. Dark Samus? That's cool because I can believe that a horrible, semi-sentient mutagen could corrupt an already corrupted, powerful being into mimicking something it came in close contact with (Samus's phazon suit). And entire planet that has a dark dimension (or whatever) of itself? Eh...I...guess so.