I think the whole Adam and Sam as Michael and Lucifer dialogue didn't fit. I felt that if Dean was Michael then everything would sound so right. That's the only part I didn't like besides not seeing them fight at all.
As for Sam getting out I think the combined powers of Michael and Lucifer could have done something. If not then maybe God just freed Sam from being Lucifer's vessel. Either it's Lucifer or it's Sam with powers because the light cracked.
I feel like Chuck could have been God all along too.