Well, I'm not sure if Mass Effect 3's ending counts as a twist, but it sure as fuck has all the elements of a bad one.
Let's recap:
The central conflict of the story so far is just a red haring. Your knew goal is to resolve the metaphysical conflict between organic and synthetic life.
You accomplish this via a machine built at an unspecified point in the past by persons unknown which, according to the very enemy you're trying to destroy, can alter all life in the galaxy on a molecular level in an unspecified way. And these mysterious past architects left control of this device to whatever dopey fuckwit happens to collapse in front of this particular command console, which apparently nobody has ever done before.
How do you use this machine? Well that depends on which mode it's in.
You can destroy all synthetic life in the galaxy, by blowing the fuck out of a tube with your gun. Keep in mind that nobody ever tells Shepard to do this; he or she apparently just deduced that, unlike most machines, blowing this fucking thing up will activate it, as opposed to, you know, blowing it the fuck up. An alternate interpretation would be that the good Commander has finally cracked, and is committing suicide via demolition and hopping to take the Reapers with them.
You can gain control of the Reapers by grabbing a pair of handles and letting the machine disintegrate you. You would think such a thing would certainly kill you, but I guess not. Oh, wait, it DOES kill you, it just also gives you complete control of the Reapers... somehow. "Trust me Shepard; what have I ever done to suggest I shouldn't be trusted. It's not like me and my colleagues have slaughtered countless numbers of your people or pushed you to the brink of extinction. Would I lie to you?"
But wait, there's more. The best option is to take a running leap into a giant green laser beam, which merges all organic and synthetic life in the galaxy... What? So everybody is just half robot now? And the reapers are apparently half organic? How is this even going to work? How does this fix anything? I thought the reapers were built out of liquefied people anyway, aren't they already sort of part organic? Are you just gonna magically transform EDI into a cyborg by replacing her internal organs? Would all children born be cyborgs now as well? Are you accounting for single celled organisms and bacteria, are they now "Synthetic" as well? Don't people with cybernetic enhancements already count as part synthetic? The catalyst said so just a moment ago. This fact hasn't stopped the Reapers so far, why would this change their mind?
And no matter what I do, the Mass Relays will explode? Just ONE Mass Relay blowing up caused an explosion comparable to that of a super nova. Even if we all survive that explosion, the best case scenario is that we all starve to death. Earth couldn't support this huge galactic armada in it's prime, let alone after what the Reapers did to it. That doesn't even account for the fact that some species, like the Turians, can't even eat the same food that humans do.
Why are the reapers even doing this?
Well, as it turns out, the Reapers, a race of synthetics, kill all space fairing species every 50'000 years, so that those same species will not be killed by synthetics... (Yo dawg, I heard you don't wanna be killed by synthetics, so I made some synthetics to kill you, so you won't be killed by synthetics)
Even if we assume this broad, unsubstantiated claim about all synthetics eventually destroying their creators is true, it doesn't change the fact that THE REAPERS ARE SYNTHETIC! By their own logic, they will eventually turn on organic life and wipe it out. This is fucking madness!
http://tvtropes.org/pmwiki/pmwiki.php/Main/InsaneTrollLogic
I'm not even sure if this fucking thing counts as a story, let alone a twist, but it had all the effects of a bad twist; it comes right the fuck out of nowhere and lays waste to narrative coherence entirely.