What I would recommend is basing it around an uncontacted world to start with and a war between bands of primitive humans and exodite eldar. Then, each race has to discover space flight or build a space ship, and once they've done that they establish contact automatically with the rest of their race. Humans and eldar can become loyalist or traitor (or craftworld or dark eldar), and then study their side's tech blueprints to get them up to date technology-wise. They can also summon their side's real forces into the battle, a bit like the Mercurians and Infernals in FFH. You could also use the same hell-terrain to represent the taint of chaos. Barbarians would be feral orks, and then later on proppa orks would start arriving from space.
This way you don't have many races to think about, but you could create different civilisations of humans and eldar like the vanilla civs. You could even just start off by making the humans.