For me it goes MP1 > MP2 > MP3
But MP2 is just barely better than MP3. Both fall way, way short of MP1 though, which is just an unbelievable experience and my personal favorite game ever. Level design, graphics, weapons, puzzles, and the methods of storytelling were all just simply amazing. MP2 was solid although it didn't really do anything new (the new visors were cool but underutilized). The ammo system was slightly annoying and the use of light/dark worlds was a weakness, Nintendo likes to use that game mechanic in place of new and more creative ideas. And like others have mentioned MP3 didn't necessarily feel like a Metroid Prime game, although I'm ok with that because they needed to mix it up a little bit. What I have a problem with is, basically, how uninspired the game felt compared to the previous 2. Almost like they were just going through the motions to push out a Prime title for the Wii. The controls of course were awesome, and Bryyo was amazing and they should've done more with that planet. The Pirate homeland was also pretty cool but other than those two the level design was lacking.
