Kinda bringing back a long dead topic here but it's less than a month!
Halo Wars takes place in 2531, which is twenty years prior to the events of Halo: Combat Evolved. Like you all said, it doesn't make sense for the Flood being in the game considering they weren't found on Halo until 2552.
There had to have been some reason but what it is, I'm not sure. I think it would have been best to keep just the Covenant. But I haven't played the full game yet so I'm not sure if the rumors are true.
A1C Peck