I agree with many others here that the flood in 2 and 3 were just awful attempts to build on what was a well thought out and well executed idea in Halo:CE
Yeah, in CE I liked it. First off, it just flowed well IMO.
second, it helped move the story along, and the presentation in the first level in which you encounter them is pretty darn good story telling in my opinion. Even though I have watched it a hundred times and the shock and awe has long passed, I still think "This was so intense the first time" and with a re-playable medium of story telling like video games, that about the most you can ask for.
third, it was a game changer, and a good challenge on a harder difficulty.
"Yeah, Im halfway through the game, I think I have this covenant killing thing down to a science. Kill the big guys, then mop up the little ones. dare I say I WIL PWNZ U ALLZ! haha, lol, yea I think I got this under con- HOLY ****!! WTF ARE THOSE! OH **** THEY ARE EVERYWHERE! OH ****! Oh ****! Oh ****! GET AWAY FROM M- WHAT THE ****?!?!?!?!?!? WHY DOES THAT ONE LOOK HUMAN?!!?!? IS THAT AN ELITE?!?! I CANT BELIEVE THIS ****! WHAT IS THIS? WHAT, NOW THEY FIGURED OUT GUNS?!?!?!?!?"
(for more humor, imagine the voice of the furious little cinnamon bun from Dr. Tran. (see youtube) saying all this)