Well in Cortana's case, the mission didn't have a designer for the longest time, which is probably why Cortana is suddenly "all better!" and the layout is confusing. Aside from that, the Flood in Halo 2 was I think a step down from CE and 2, despite the ability to instantly convert forms. I don't have a hatred of The Library but Quarantine Zone and Juggernaut are definitely my least favorite levels in Halo 2.