I felt that the more Halo games there were, the less interesting the flood got.
In CE, it was very startling the first time encountering them. The anticipation leading up to the first encounter was very well done, and the fact that Elite flood didn't really resemble its "infected host". Once I saw the human counterparts, it was a shock. Even today, the build-up to the floods first appearance is done very well. The flood them selves are also pretty unique compared to the covenant. An "in your face" ass strategy and those things on their arms that could kill you if you weren't paying attention.
In 2; I liked how they updated the flood's way of infection, but hated the difficulty. Don't get me wrong, its still hard getting though the Arbiter's levels on legendary because of a single infection form, but the fact that the sword could stop a flood from getting back up kind of nuked the difficulty curve. If anything, the only thing I wish is that they either showed MORE flood driving vehicles in later stages/games, or just take it out. A perfect way to make the flood seem even more threating, and it wasn't touched on much.
3 Didn't do the flood much justice. Sure it was creepy to see them infect LIVE hosts and uninfected corpses rather then the whole "incubation thing" they did with Keyes, sure adding the Brute forms made them seem more threatening, but if anything that killed the threat of the flood: it was the Tank forms and the Gravemind. It was never explained what the Tank forms were (i think only one of their forms is called tanks, but I don't know, and thats how much I care about them), but it just seemed like they had little inspiration on a decent flood enemy. Also, the Gravemind. It existed in 2, but I never understood. Is there more then ONE gravemind, did every ring have one, why did that one choose to head to the Ark immediately? Personally, story wise, I never understood it.
I also felt that they nerfed the flood the more games they had. Very few times was I killed by flood in Halo 3, even on legendary. High Charity, the flood level in 3, attempts to mirror the Library, and almost does except for the difficulty. That and in 2 and 3, they just got too easy to dismember, which practically nuked the threat. In CE, while a flood form could only get up one or two times if its arms were in tact, it was still annoying and even felt wasteful to shoot corpses arms off, but it was better then having it come back and kill you when you least expected it. In later games however, just punching them enough and they explode like confetti.
And like Thaius said: Their appearance in Halo Wars was like someone attempting to sell furry porn at an art auction. Aside from the story side, I felt that at that point, Halo Wars was trying to be Starcraft in all but Species. While the Covenant and Human sides had an intersting story and unique game play, it just felt that the flood were too out of place.
Thankfully there were no flood in Reach or ODST (weird to say, but after Halo Wars, I admit I had my doubts about the two). But what I will say is that the flood were a unique enemy. Personally, after Combat Evolved, they just got too easy.
But one thing I will always miss is having a Combat Form with no arms follow me around in Halo: CE. That was always fun. (I call them Stumpy
)