I've just been looking at the main website for the game to see if anything new has been added and the section on diplomacy made me think. As we progress through the game we'll be forging our own relationships, alliances and enemies. From what we know about the factions and companions there will definitely be opposing sides which we will most likely have to pick between at some point.
What if the last antagonistic force and the final boss are not set in stone, but are selected via choices made by the player? Which ever faction you have the least standing and influence with is the one that comes gunning for the party in the end? Maybe a former Companion who has left your party and been powered up to boss status via magic enhancement, steampunk armor and weaponry or whatever their faction specializes in.