While some things have changed, others have not. I do believe Sun and Jin are married in the sideways timeline. I also believe we have been shown the good/evil dichotomy since the beginning, but I don't think it's only the Judeo/Christian version.
In every interview I've heard with them, Damon and Carlton have stated clearly that they were forced to rewrite the Boone and Shannon backstory because Maggie Grace was not available. I'm sure that is not the case for everyone we didn't see on the plane, but I am sure it's true about Shannon. They also said they hope she might be available at some point. They also stated that a lot of the focus this season will be on the consequences of trying to change things, which I guess is back to the free will versus fate idea.
I do agree that Richard's chains may not be physical chains; that's something I had not thought of.
In any case, I am happy to speculate and research, but to also leave the story telling to the storytellers. They haven't disappointed me yet.