Oh. I was under the assumption I could "waste" a faction, "ignore" a faction, and "side" with a faction. Sided factions be my cool Vegas buddies. I guess I was horribly, horribly wrong.
Independent Vegas is just that - independent. You don't run the whole world, you merely run Vegas. Everyone else is content to ignore you and go about their business, or develop a trading relationship with you. If you were meant to rule the Mojave, the quest wouldn't be "No Gods, No Masters", it would be "I'm God, I'm the Master" since you're technically ruling then.