Funny xD I just beat Prime, and I'm about half-done with Echoes, and trying to negotiate using the Wii (my brothers have taken it over recently).
So far though, I say Prime is my favorite. As a story period, it's one of my favorites, right up there with Portal or any of Asimov's work. The music is sublime, the graphics are pretty impressive even today, the atmosphere is fantastic... and Prime gave me one of the only moments in a game where I honestly just stopped playing and stared at the screen for about a minute. That said, the Torvus Bog in Echoes is very nice looking, and I love the music for it. I cannot wait to see Corruption, especially since I read some of the interesting bits on TV Tropes. Gotta say, I'm itching to see what the hell would cause someone to puke Phazon, let alone shrugging it off like they described.
I did a straight shot through the Magmoor Caverns, and was on my last energy tank when I finally got to the elevator. Blasted my way through the tunnel, then this [http://www.youtube.com/watch?v=hrVoQSdw8Zs&feature=related] starts up, and I'm treated to that little cutscene showing of the Phendrana Drifts (if it helps, I am a winter freak- snowy areas are just heaven for me).
It's rare I'll call something beautiful and mean it, but given my tastes... Yeah, Prime's just beautiful. The scenery, the scans (I had to read the 'Metroids are not pets' thing twice to confirm it was real, and some of the Chozo messages were quite sweet), the overall atmosphere... the only thing Echoes did better was when it came to boss fights. Prime made you work, but you feel like a monster truck that walks like a man when you beat some of Echo's bosses (LOOKING AT YOU YOU FRIGGIN... DRAGONFLY THING. It took a ton of hits and finally dying once before I realized you could only lock on when you were facing its back.)
... wow that made me sound like more of a fangirl than I am.