I've been a huge gamer since the early 80's as well as a huge Metroid fan since the first one on the good 'ol NES, and let me tell you that Metroid Prime & Metroid Prime 2: Echoes are two of the best games ever developed. Both are masterfully and intelligently crafted with such an incredible level of detail and immersiveness that has never been done before. I LOVED both of them and I thought Dark Aether from Echoes was VERY well done. Dark, brooding, ominous and it allowed a level of puzzle solving and exploration that was absolutley stellar. I really, really enjoyed Prime 2 and I'd even go as far as to say that it topped the unprecedented first Metroid Prime in every possible way. The gameplay for both games were amazing and the fun factor was through the roof. Metroid Prime 3: Corruption is definately looking like it's going to top both Prime 1 & 2 on a grand scale. I can't wait!
As far as the story goes for both Prime 1 & 2, Dr_R is absolutely right. The story is not so obvious and it isn't presented to you in a manner you can't miss like just about every other game. You have to do your part to find out what has happened and what is transpiring. That is part of the charm of the Prime series, it has a lot of mystery and takes investigation to find clues as to what's going on and what needs to be done. Actually, this is true for all Metroid games, but never before on the level of the Prime series. From my experience, people who have said the story was weak and boring skipped a lot of the content or tried to rush through them. It's a real shame. Both Prime & Prime 2: Echoes are probably two of the most underated games ever produced. But, everyone is entitle to their own opinion, though.
As for Prime: Hunters... I actually really enjoyed the single player campaign. I thought it was very well done. Not at the level of it's GC counterparts, but still very, very enjoyable. The multiplayer modes were always intended to be the focus of Hunters and they did a fantastic jpb with it, but still, the single player experience was a blast, IMO.
Chance favors the prepared mind.