I absolutely loved Metroid Prime 1. It's easily one of my favorite games this gen. I just finished Metroid Prime 2 yesterday and I must say I was disappointed with it. While it's not a bad game by any means, it simply doesn't stand up well against MP1. Whereas the Metroid series' trademark backtracking didn't bother me at all in MP1, it really got on my nerves in MP2 due to the level design. In MP1, whenever you found some new item/upgrade that allowed you to access previously inaccessible areas, the world was designed so that it was usually pretty easy to find where you were supposed to go. Often there'd be a nearby elevator that would take you near where you should be headed. The world just seemed to be designed in a way that logically led you to where you wanted to be. In MP2, I often found myself wandering around in circles and fumbling around with the map, switching between Aether and Dark Aether. I had no problem playing through MP1 with the hint system disabled. On the other hand, Aether's layout was too confusing that I'd often have to wait around for the hint system to tell me which area I should be looking around for an item/upgrade in. Traveling from one end of Aether to the other to find some item and then being forced to trek all the way back to where you just were is tedious and not fun. MP1's tiered sections were much easier to navigate between.
As most people already mentioned, the dark world was also rather boring. I have no problem with cliched design conventions like that as long as it's done well. Just look at MP1, you can't get any more cliched than splitting up the world into forest, fire, ice, and underwater themes. Unfortunately travelling between Aether and Dark Aether was just plain cumbersome and annoying. I think handling traveling between the two worlds in real-time a-la Soul Reaver would have been much better. Travelling to the spiritual realm in those games was so simple and quick that it made the figuring out the dual-world puzzles fun and straightforward. Watching the world morph and transform before your eyes in real-time (without any loadtimes) in SR1/SR2 was much cooler than waiting for the game to load and finish showing the same portal animation as in MP2.
The only other things I didn't like are rather nit-picky. The logbook in MP2, while better looking than MP1's, was a pain to navigate though. MP1's logbook, though not as pretty, was much easier to look through which made the artifact quest at the end of MP1 easier to deal with than MP2's key quest. I also preferred the Samus model in MP1 more. The metallic finish of her armor looks much better in my opinion. Granted the color scheme in MP2 is truer to previous Metroid titles, I still prefer MP1's Samus model. Similarly, I also preferred Samus' face at the end of MP1 more than how she looked outside her suit in MP2. MP2's outside-the-suit Samus model doesn't mesh with the rest of the game's art direction. It seems like Retro was simply trying to be more in line with the Japanese made games like Zero Mission. Too bad, I much prefer Retro's own original designs. Speaking of which, I loved the design of the light suit. The dark suit was also nice, but I really liked the light suit. On the positive side, aside from the Dark Samus battles, I preferred MP2's boss battles. They were well designed and more challenging for the most part (as were most of the games enemies). Also, on a technical level, MP2 is a better looking game, especially the textures. Again, MP2 is not a bad game, but it's pretty disappointing after the greatness of MP1.