Another thing which would greatly help the sense of unity is to create several large scale events which occur in the world and are somehow tied to the overarching story line. These large scale events would occur no matter what path you're on, but the path you've chosen will effect how you interact with those events. For example, imagine that at a fixed point in the timeline there's an army which attacks a city. Depending on your current branching path, you may find yourself in a number of positions. Perhaps you're at the front lines of this attacking arming, or maybe you've enlisted in the militia of the city and are defending it. Or maybe you just happen to be strolling through the city at the time of attack. Or perhaps you're in a distant land altogether and you only hear word of the attack. Or maybe you've found a way to prevent the attack before it even happens, such as by helping form a truce of some kind.
Sorry about dragging out an old point from the thread, but I'm late to the discussion:
For the longest time, I've had this concept of making a "real time" RPG where the player interacts with the world as it plays out its natural cycle. I most certainly agree that it would be a Herculean sized task to write out all the possibilities, but not impossible. The timeline story system I came up with I call "Nexus" as every major event is a Nexus Point of change in the world's history where the future storylines diverge. (A decisive battle, weather or not a scientist succeeds in detonating his superweapon, maybe if Hitler didn't get elected, etc...) The player can directly affect the outcomes of Nexus Events through direct intervention (Leading the Attack), or indirectly by affecting variables that influence the outcome of a Nexus Event (not healing the potential future NPC War Hero a week before so he died, also not getting the shipment of magical talismans in time to the front). Win or lose, the story continues along the available Nexus Event Paths to an eventual conclusion at the end of the timeline.
Of course, I haven't ever done anything with this system besides daydream about it. But judging from the discussion in this thread, the idea's time has come. I'm eager to see what anyone can make of it. If I ever get my motivation up to make an RPG, I'd certainly like to make one with a Nexus Event driven storyline.