But Felix, you look at it through a canon junkie's (not ment to be offensive) point of view, I look at having more leaders or factions as getting more game content for your buck and having better, deeper gameplay with more choices to make, which is what Halo Wars really suffers from, lack of depth.
I look at the flood as what they are; flood. They aren't a real faction, their only tactic is numbers and charge. ES said they "wanted them to be scary", as the flood is by nature. Unfortanitly, the flood are only scary when you are a one-man person in a huge war, or FPS. They just aren't needed to make it the game it should have been.
That's not true, their led by a collective conscience, a Gravemind who is supposed to be this all knowing being. If he's so smart, I'm sure the Flood is capable of more than just charging. You think of the Flood in just their feral form, infact the a cool thing about my idea is they do start out as a feral form at the beginning of each game, only able to make Infection and Carrier Forms, but later, as they gather biomass, in the midgame they become what the Flood were in Halo Wars, somewhere between feral and Gravemind states, where they have a Proto-Gravemind. I'm saying it works into canon well enough, that's why I bothered to do all that, to prove it could work, and add more game content so more people will play. Also your right that it's hard to make them scary in RTS form (even though I thought my Gravemind and Master Root uber units, or a group of fully grown Juggernauts would be pretty scary) but why dose it matter? RTS's are about stratagy.
If your really that against a Flood faction then just don't play them, infact make that an incentive to want to crush any jerk who decides to play as the Flood. Lol, make a clan called the Alliance, where both people who play Covies and Humans can join to plot stratagies against the Flood. just a cool thought, putting aside differences to fight a greater threat, whatever
and to Offensive Bias, it's true that the lie was before Halo Wars' release, but were're currently in the time before Robot's next game is released, think about that.
EDIT: I don't think a Forrunner faction could work realy well, if there's going to be a new one, it'll be the Flood no doubt.