Pfft, I actually like The Library. I used to dislike it, but it's definitely grown on me. It's mesmerizing, and Halo CE flood-only combat is actually pretty amazing once you figure out that the Flood aren't supposed to feel like Covenant in combat; fighting the flood is kind of a dance if you're actually doing it correctly. It's unique and interesting.
I hate the level Cortana, though, on tons of levels.
First, because Halo 3 flood combat actually does irreperably suck; high damage/low health/slow and disjointed approach means the absolute best way to fight them is lethargically. It's practically the polar opposite of Halo CE's upbeat flood.
The atmosphere would be far better if it brought out High Charity a tad more; by almost completely covering everything and giving exremely limited open views, you ruin opportunities for good juxtaposition. Optimally, they would have had some interior areas be a harsh flood hive, but also leave some open Halo 2-style vistas sticking out from it. By presenting what the thing used to be, you allow the changes to better distinguish themselves. You build contrast. This is one of the things the first Halo does brilliantly (albeit through slightly different means) but which most of the others fail miserably at.
Writing. Halo 3 takes a lot of crap for storytelling anyway, but it should, because unlike Halo 2 it's storytelling problems weren't the result of development time fail. While some of Cortana's lines in that level may yet be interesting depending on where canon expansion goes, even if the delivery was annoying, Gravemind seriously needed to stop letting Bungie's writers murder his awesome character established in Halo 2. And I'm a little sad that it's some conveniently placed Covenant reactor that was detonated and not In Amber Clad's.