My biggest issue with Prime 2 is simply the whole "dark world" thing it did.t of.)
The dark world concept was actually suggested by Kensuke Tanabe, the story writer for A Link To The Past. Personally, I thought it was an interesting concept. It was definitely a pretty forboding place, and definitely fulfilled the objective of being a place where you didn't want to be, even as you gradually became powered up.
As for the rest of Prime 2's environments, Retro's direction with Aether was to create a more believable world (as opposed to standard video game environments like ice/fire/vegetation), albeit one that is dying and is going through a large scale conflict (or has gone through one).
I brought up the analogy of Prime 2 being Metroid's Majora's Mask before, but I did not elaborate on it. Its similar in the sense that they are the follow-up to the the most critically acclaimed game in the series (Ocarina of Time/Metroid Prime), and both released about two years after their predecessor.
In regards to the respective mythos of each of their series, both are oddballs. In Majora's Mask, the Triforce, Zelda, Ganon/Ganondorf, and the Master Sword are not part of the plot (Zelda does make a cameo via a flashback though), and the game takes place in an entirely new world, and basically has no impact on the history of Hyrule.
Prime 2 has the Space Pirates and Metroids taking a back seat in the game, with the Ing being the primary antagonist. It is also only one of three games in the series not to have Ridley in it. The ammo system and the alternate worlds concept also make the game stand out relative to the rest of the series, in addition to, the presence of a multiplayer mode (the only other game to feature this was Hunters).
When Majora's Mask was initially released, the game was bashed a lot for being "too different" compared to Ocarina of Time, and the difficulty of the game as wellwas used as a detraction point. Similar points were met with Prime 2's release.
With time though, Majora's Mask is now seen as among the strongest installments in the series. Prime 2, being a part of the far less popular Metroid series, has taken much longer for others to see the strengths of it relative to the rest of the Metroid series. At the very least though, more avid Metroid fans do see it now as the stronger (or better) sequel between Prime 2 and Prime 3. In terms of atmosphere, its definitely up there with Prime 1 and Super Metroid.
It is basically the 3D analog to Zero Mission. It is basically for the avid Metroid fan, at the detriment of other game players. This is why I see many people prefer Prime 3 and Fusion over Prime 2 and Zero Mission, despite the latter ones being better as actual Metroid games.