I played Metroid Prime twice, and Echoes twice. Echoes was the more enjoyable one to revisit because the first one was such a pushover in the 2nd run: levels, puzzles, and especially bosses. Prime1 was probably my turning point that made me sick of the familiar Fire/Ice/Green Zelda themed areas. Echoes provided satisfying challenges in greater amounts, even at the base difficulty, more interesting 3D puzzles (i think Nintendo's best to date), scarier enemies, and yummier boss fights. Playing Echoes the first time thru with the hint system disabled, it was an exploration-gamer's dream, where you progressed entirely by discovery/strategy/merit (wasn't Super Metroid like that?) -- the detailed map and your power-ups provided all the hints you needed to access new territory and make progress, and dead-ends weren't wastes because it's a plain fact something is hiding and waiting to be found. Echoes's stage modeling/architecture (aside from the plain triangular hub world) was more wickedly alien, making me glad I don't have to sit thru more Fire Temple/Ice Temple repeats.
Prime1 is notable for being exciting from the very beginning. But it takes a big nose dive once you enter the Mining area, with no real spice until you reach the last string of bosses. I played thru cuz, well, it's a new game with new things to see. I say Echoes took the opposite route with delayed gratification. Starts off unexciting with a, surprise, Mining area, but steadily ramps up all the way to the end with a stellar curve. (Then, wink-wink, MP3 comes out and is designed to flow a little more like Prime1. What is this, Indiana Jones? The Prime series and the Indy movies are alike, when you consider the dark/strange/intense direction Temple of Doom took, only to zig-zag back to desert-archaeology theme in Raiders/Crusade)
Granted, Prime1 gets the respect points for doing its 3D Metroid thing first, but it has 3D Zelda to thank (for better or worse). It's a slight misfortune that Prime1, back in 2001, was only the 3rd 3D explory action game I've played, after OoT and MM, and I went thru the game with the Hint System on by default. I might have been more fond of it without the Hints, I just wasn't fully accustomed to Nintendo's 3D adventure design philosphy yet. Now, hand-holding makes me smolder with rage. I'm not a big fan of 2D Zetroid nor 2D Melda, my mind doesn't wrap around large 2D maps well, unlike 3D enviros.
I'm buying the Prime Trilogy, but probably won't touch it until I finish Conduit/DeadlyCritters/MadWorld/Overkill Director's Cut/Kororinpa2/DeBlob/BoomBloxAssParty.