My friend Amanda and I came up with a pretty good theory as to how the writers will tie the alternate reality with what is going on with everyone on the island:
Something struck me in this last episode. Sawyer was sitting in the car with Miles and he said, "I came to a point in my life where I was either going to be a criminal or a cop…I chose cop." The idea of there being one decision in our lives that determines the course of everything after that decision was introduced in "The Incident" when Jacob visited the candidates and influenced a life-altering decision that they had to make. That decision led them through a difficult life and also led them to the island.
If things continue as they are, it is safe to say that Jack will be "the new Jacob" (if you need more explanation on why I feel this way, I'd be happy to oblige). So, let's say that Jack, as "the new Jacob" visits his friends and influences their lives in a DIFFERENT way. What if Jack, as "the new Jacob", has visited his friends and led them to make a decision that led their lives down a better path that did NOT lead to the island?! That's something that Jack would do.
This would explain why everyone seems to have better luck in their alternate reality: Kate not going to prison
Sawyer being a cop instead of a con man
Sayid never having lost touch with Nadia (although they're not "together")
John Locke still being with his special lady friend
This would ALSO explain why in "LA X", when Kate hopped in that cab and saw Jack, she seemed to recognize him (because he had visited her at some other point in her life to send her on a different path)
Also, keep in mind, in John Locke's alternate reality, meeting Jack was the catalyst that ended up bringing him closer to his wife.
This theory does, however, have a few holes:
If Jack is acting as Jacob, then why does he still exist in the alternate reality?
If Jack influenced his friends to lead a better life, why is Kate still a fugitive. Why is Sawyer still hunting for Anthony Cooper?