This tread and pool are based on spoilers from achievements. We don't know if they are mutual exclusive, but we know that there are three joinable factions:
Minutemen - They seem to be a factions fighting for independence and even their name is based on soldiers who fought against the British during American Revolution, also called Minutemen. We don't know against whom they are fighting, but it is most likely the Institute
Brotherhood of Steel - We don't yet know if they are Lyon's BoS or the Outcasts, but we all know what BoS are ;P Most likely, they are invading the Institute for their advanced technology
Railroad - this faction appeared in FO3 and are abolitionists who free slaves. They are mostly specialized in saving Androids from the Institute
Institute - not a joinable faction, but seem to be the most advanced and ruling faction of Commonwealth... and might be the enemy of the above three factions as well as the prime enemy of the MQ
Well, two of them fight the Commonwealth and BoS will most likely fight them as well. So, what do you think they will be about and whom do you think you will support?
Personally, I think that they will be (and i hope they are) mutualy exclusive and that each faction will try to take over Commonwealth: Minutemen probably want to create an independent state, the Railroad might want to create a state where Androids and humans leave in harmony (or an Android state) while the BoS will want to conquer it for its technology... and maybe add them to their empire, if they used their position at the end of FO3 to take political control over Capital Wasteland.