I've got a non-Black Ark theory myself and it focused around the Ark Ships leaving before the end of ME3.
http://forum.bioware...4#entry20315800
I do find it a little silly to see so much mathematical nitpicking a science-fantasy game. This isn't really sci-fi; that ship sailed when ME2 started. It's probably going to come down to "A space wizard did it." I'm not faulting the more mathematically inclined posters for having a big case of "What the frak?!?" The series was always iffy about their "science," but I can see why it's going to be jarring for some, regardless of the explaination given.
I don't know, I found Shep coming back from the dead after being suffociated, caught out in space and then found crashed on a planet harder to swallow than intergalactic travel. The latter may be contradicting some of the lore, but the former was bat guano crazy.
I'll take them expanding the current lore over something that contrived again. It was like they went, "A coma is too stereotypical and it isn't "awesome" enough. I know, let's have Shepard come back from the dead after 3 years!"