I hope they don't take the WAR route, which is to make the player a wandering independent character whose questing and fighting in any realm help to gain control of it. It would work however. It would be a good system if they wanted to include the other races. Questing however becomes stricter, mission-based, stay with your squad. Or you could perform non-combat functions if the race allows.
I was wondering if the system could be where the player can only join the Imperium. But that would be unacceptable to many people.
How the hell are you going to have an independent Tyranid or Necron? Isn't oneness like the religion of the Tau? So what room is there for independence for the player? And Orkz and Eldar don't seem to give much leeway for starting a new guild, Orkz giving much more than Eldar in comparison. I'm not sure about Dark Eldar. And I doubt there's independence for players who are Chaos. Although as a human, they can always join Chaos as a heretic.
So what if you joined the Imperium as a normal Human who can join the Imperial Guard, or go it alone. I'm not sure if this is how it works, but after serving for some time, you could join one of the other areas in the Imperium or stay and rank up in the Imperial Guard, giving you access to better equipment, greater choices, more information, and higher command over the army. Other branches include the Adeptus Astartes, Adeptus Soritas, Adeptus Mechanicus, and of course, the Inquisition. Go-it-alone, or join-a-group, paths are Mercenary/escort, Merchant/freighter, Explorer/scientist, Gangster, and Cultist.