Lots of things bug the living heck out of me about World of Warcraft, but one of the bullet points on that list is the fact that there’s still no way for an individual to switch factions. It just doesn’t happen, despite the fact that we know there are members of Horde races in the Alliance (and vice-versa) and plenty of space for disagreeing with your factional stance. City of Heroes got this right ages ago, and that was a game where the factional split was based on actual morality, not just political alignment.
Personally, I think every game with factions should offer a mechanism to allow players to swap their faction. There should be no hard-and-set uncrossable faction lines. Even in Star Wars: The Old Republic, you should have the option to make a reformed Sith or a fallen Jedi if you so desire, and classes like Bounty Hunters don’t even have factions in the first place.
But perhaps others feel like that would erode some of what makes factions distinct. Having watched people develop strong factional identities in games like Final Fantasy XI (which encouraged you to swap factions) that rings false to me, but what do you think? Should every MMO with factions have mechanics to switch factions?