I love how all-over-the-place different the personal rankings of the Prime series are!
It also supports my own opinion of Prime 1 = Prime 2 = Prime 3. I love them all, couldn't rank them because all of them have their own high points and, yeah, all of them also have different flaws. (My nostalgic high point in the series is still Prime 1, but I can't say Prime 1 is better than Prime 2 and 3 because if Prime 3 was the first one I played for example, that would be the one I'm nostalgic for... At the time it was released, Prime 1 was just the perfect storm and a landmark videogame, the others followed the basic formula so there's that.)
Prime 1 nailed atmosphere and exploration. Prime 2 nailed difficulty and feel of isolation. Prime 3 nailed story and pacing.
Prime 1 felt a bit formulaic at times. Prime 2 missed a bit of the atmosphere which made Prime 1 so very "Metroid in 3D". Prime 3 showed some signs of fatigue and felt a bit "been there done that" even though it is still an excellent game.
(Motion controls are a matter of taste. I prefer them so much that I couldn't imagine playing Metroid Prime on Gamecube again after owning the Wii collection.)
I am glad Retro could take a break from the series because when and if they return for another Metroid game, it will a) feel fresh again and b) they might have new ideas and use better console tech for an even more atmospheric experience and enhancements.