As we all know, there will be a new character appearing in later DLC. People say he will be a follower; others a last antagonist. I think both are actually true. I don't have a clue how he's going to switch from one to the other, but i do know the outfit he wears means something. They say he is under the banner of the old world. This MIGHT mean he could POSSIBLY (forgive any spelling error) that he could be Enclave. They have been known to keep old world values and culture. I think that the final battle will be between you and his army in the great divide. That's when the choices you made come in. Your allies could depend on your choices, like what faction you chose, your reputation will also count when it comes to your allies and enemies (ex. Bad rep with the followers of the Apocolypse = more enemies).

Another outcome is that it will just be a one on one, courier on courier. This would mean that NOTHING you did in the game would effect that main quest, but your choices could become more important in later DLC or in sidequests. That doesn't mean you should make the right choices, because there are no right choices. It depends on your point of view who you think is better.

If I ripped any of your ideas off, I did it unintentionally.