I think it comes down to tone. Comparing Halo to Halo 2 is like comparing Aliens to Star Trek. They're certainly similar, but the first is much darker and has a certain atmosphere to it.
I remember finding the Flood for the first time, and it had a long, tense build up to the reveal, with a genuinely creepy pay off, and between the music and the maze like level design, it just felt imposing.
Where as Halo 2, they go "SURPRISE! Floods here :3"
No Halo game after CE has really given them the red carpet that the first reveal got.