This is a bit dated, but I was thinking the other day about why Metroid Prime 2 ended up disappointing me. And I think the answer was how dark Aether was handled. Remember the first time you got to dark aether in the agon wastes? It was dark and foreboding, and a very dangerous place. You had to plan your moves carefully or the atmosphere would quickly eat your health. You really didn't have time to look around and notice that the landscape was kinda drab.
But as time went on, dark aether became less thretening. Once you got the dark suit, the dark atmosphere was no longer a threat, but more of a nuisance. You no longer had to plan your moves or worry about your health draining. You had more time to look around and notice that there really wasn't much to see there. The dark side was no longer threatening, and really became rather boring.
Then you got to the Sanctuary Fortress. The dark side of the fortress was called The Hive, and was supposedly the Ing stronghold. But when you transfered over there, there really wasn't much at all. It certainly didn't feel like their stronghold, as if it was, the Ing should've been swarming all over you. In fact, the light side was almost more dangerous than the dark side. I think it would've been a good atmospheric idea to leave the light side mostly devoid of enemies - maybe a few of the security droids and those annoying floating orb enemies. But when you went to the dark side, the enemies swarmed. If they did that though, they would've probably had to redesign the area to keep your travels in the dark side relatively short. But that would've created a great atmosphere that would really match the story of that area. You see a portal, take a beath, and dive in - just hoping to emerge alive at the other end.
So while I thought MP2 was quite good, this one aspect was quite poorly handled. It truely is a shame, as it could've been the game's strongest point had it been handled well.