Brutes were not a part of Jul 'Mdama's Remnant. Plus, they were nearly wiped out through fighting anything they saw. Including themselves.
Drones/ Y'anme probably left the Covenant or just returned to Palamok, not wanting anything to do with anything.
Flood. Requiem (Most likely) did not have Flood containment facilities; therefore they were not in the game. A Gravemind took hundreds, if not thousands of years to fully develop to the levl of H2's GM. They will most likely not return for a while.
Monitors. The game was not set on a Halo, therefore no monitors.
ODST's (I make up my own explainings for these kind of holes) were deployed on a different part of the Infinity that the Master Chief and Crimson was not deployed on. Though Halo: The Flood shows how all the Marines you see in Combat Evolved were in fact ODST's, just wearing non-standard armour. So it is possible ODST's were encountered but not in their Helljumping armour?
A) The story was explicitly about Chief and Cortana. The story was not about the UNSC. Plus, they had a prescence in a few of the missions anyway becasue it wouldn't make sense in the first and last few missions.
Master Chief wasn't on Infinity for long; a day at best. Plus, simple game/ technology limitations block large battalions of hundred+ forces taking on the enemy like in Halo Wars or StarCraft. The Halo games have never been about large battalions, they were always about being part of the smaller teams. If you get what I'm saying. Halo 4 has had no more or less AI in any one location than the previous ones.
All in all, I'm getting a 'I want a Halo 3 campaign in fancy graphics" feeling for you, that the actual story doesn't matter as much. Meh, if you took time to think about the story or even read the EU Novels, yo might realise some of these?