I think there will be Flood. I wonder if we will have to fight Brute infested Flood. I don't remember fighting any in Halo 2, and I can't really play campaign that much because it always fails to load the levels. I know that the Hunters can't get infected because they're not just one creature, but what about Brutes?
I don't remember anything about the Brutes not being able to be infected, but Grunts and Jackles can, but they turn into carrier forms rather than combat forms.
And about the hunter, It's made up of a colony of eels, all writhing inside the armor, and, I can only assume, one infection form could only infect one of the eels, not doing to much to the whole hunter.
it wouldnt be able to effect even one, since it attaches itself to the spinal cord and injects chemicals in to control the creature or person, then sorts through the creature memory for useful information and discards the rest, a process that really sucks, in rare cases those infected have been known to gain some control for small periods of time (private jenkins) and its unlikely we will see brute hosts but its possible, also if a creature dies it cannot be infected