For me, it's the Library, mainly because the Flood tend to use guns more CE, and the open spaces mean you can potentially get attacked from all sides. Not to mention the fact that Elite forms LOVE playing dead (thank god scoring gives this trick away). The holdout sections are by far the worst part mainly because there's no way to speed them up. Plus, the monotonous visuals make it easy to get lost when playing with old graphics (thank GOD for the Anniversary remaster adding arrows to the floor).
I honestly find Cortana more annoying than hard, mainly because of the confined spaces limiting maneuverability, the overabundance of Pure Forms and the fact that the aesthetics make it hard to navigate. There is one weapon that makes Cortana more tolerable, though, and that's the Brute Shot. If you manage to grab one at the end of The Covenant or during the level itself, you're pretty much set for the entire level. The Brute Shot's melee 1-shots Pure Forms (even with Mythic on) and dismembers Combat Forms pretty well, plus a well-placed shot can knock Ranged Forms off the walls and blow apart several Combat Forms at once. The Brute Shot makes the whole level so much better to play, as long as you know where you're going.