EmCee, I didn't like Metroid Prime because:
-Game was filled with backtracking, I must've backtracked through that stupid lava area about 30 times during a single course of play
-Control scheme felt counter-intuitive
-Awkwardly positioned fetch quest at the end of the game
-Too much focus on stopping to scan everything for backstory
Not to mention, the whole thing felt soulless... for me, I wasn't playing for fun after a certain point but just to get it out of the way. Absolutely loved the music though, especially the second part of the Phendrana Drifts.
*disclaimer: I'm a 2D, retro-gaming whore who loves the traditional Metroid games.