Just add a fourth option besides Red, Blue and Green where you tell God to go **** himself and you (and the rest of the galaxy) go down fighting. Finish that with a cut-scene where several thousand years later some new alien race finds one of the time-capsules explaining everything and giving them a better chance to end the cycle. And voilà, you have a better ending than anything Casey Hudson came up with.
There are so many things wrong with the literal Deus Ex Machina we meet at the end but what I really can't understand is why Shepard would simply accept the choices he's given. This God we meet makes Hitler look sane, sound of mind and charming by comparison.
I mean when God gives you this kind of logic it is time to become an atheist.
Also... artistic integrity