You mention that you can still unite them to get the ultimate ending, which sounds kind of like Skyrim's faction quests mixed up with the multiple endings you can get in many games rather than completely different plots (correct me if I'm wrong!). I'm more thinking of a game where there are two or more sides you could join up to, but that you could only join up to one side for the rest of that playthrough. Basically forcing you to restart from that save if you were to want to check out the other plots available. Imagine if you could be a freedom fighter who frees the world from Shinra... or if you could join Shinra and then go up the ranks there and get rid of those freedom fighters. Two completely different stories... in one world/game. One interesting take on this is Crysis and Crysis Warhead, which saw the same plot from the view of two different good guys who were on the same team. I thought it was pretty well done, but couldn't help but think "How awesome would it be if a company did that without me having to pay for two games?"

One simple way of looking at this would be that most RTS allow you to play as numerous different races/factions, each with their own storyline. Obviously the plot takes a massive backseat in such situations, so I'm wondering if there are any games like Skyrim/Mass Effect where you could actually just join the bad guys and have a completely new plot develop.