I liked Prime 3 better than Prime 2.... Ammo for dark and light beam was weird and I always disliked using ammo weapons including bombs and arrows in Zelda. The color scheme in the beginning of the game was also very bland coloring compared to Prime 1 and Prime 3. I never finished the game, though and won't have the ability to anytime soon since my Wii can't play Wii games (plays GC games though...) and I only own MP: Trilogy and not Echoes. I think I stopped after beating the boost ball boss which was actually easier in Trilogy than the original but I wouldn't know >_>
But I probably also disliked it because IR pointing for Echoes was really bad compared to Prime 1 and Corruption for some reason. Maybe it's because I used a new TV for it.
Edit: Since I only played the Metroid Prime trilogy from Retro and never finished Echoes, I would have to choose Corruption!