I don't understand the hate for the Flood. I thought they were an awesome, sinister enemy that was well introduced in the first Halo.
They made for an interesting mix of combat styles. The Covenant would use tactics and cover and generally be quite sneaky whereas the Flood were absolutely fucking nuts lumps of flesh controlled by parasites that just threw themselves at you.
Watching the fights between Flood and Covenant was always fun as well. Playing on any level of difficulty below Legendary though and the Flood basically overwhelmed the Covenant. However, play on Legendary and the Covenant Elites were fucking unstoppable.