When Ghor started attacking Samus' gunship on Elysia, I was sure that he was going to possess Samus' ship and use it against her. I thought that what was Ghor's ability to interface with mechanical devices was leading up to. As awesome as having to fight your own ship would have been, the Ghor fight was pretty good as it was, so I can't really complain.
I have to admit, I'm not too fond of Skytown. Okay, so the final part where you have to defend the Spire from a Space Pirate attack was cool, and Helios was incredible, but the area in general bored me. The layout was really repetitive and the enemies weren't too interesting. I have to give Retro credit, though; the Metroid breakout was really atmospheric, even if the actual Metroids were total pushovers.
Holy crap, the bosses are incredible. The Metroid Prime games have always had excellent bosses, but this game just pushes it to the next level. I thought that a few of the previous Prime games had bosses with too much health for their own good, but every fight so far has been memorable and none have gotten boring. I haven't had sweaty palms in a game for quite some time.
Berserker Lord was a pretty good introduction to using the aiming controls properly. While the rematch with him in the Chozo Observatory on Elysia was kind of random, it was fun to see how far I had come since my first fight with him. I would have rather seen a Torizo or something there, though.
Meta Ridley was incredible. So far, that's the defining moment of the game. I even liked how Samus defeats him; by jamming her arm cannon down his throat and opening fire. In-freaking-credible.
Mogenar was the only boss I really found annoying or unfun to fight. It was just tedious, since his weak points are only open sporadically, especially when you're trying to time a Hypermode activation. The appearance of the Leviathan Seed was amazing, though. It looked so organic and alive. Simply incredible.
The Metroid Hatcher was pretty disappointingly easy, though. Seriously, after the challenge that was Helios, the Hatcher was pretty pathetic. I don't think that thing touched me more than once in the entire fight; the only damage I sustained was when I stupidly threw myself off the platform. The one thing I can say in the Hatcher's favour is that the fight was a surprise. I was just going to Norion to pick up an Energy Cell... and holy crap, got ambushed by a boss.