I think that things have been building for a Jack vs. Locke showdown from day 1.
And Jack has still not came face to face with Smoke Monster Locke, and this to me is because Jack is the candidate, he was the man of science who had no belief or faith that the island was special, but now he increasingly is turning into the man of faith. He will be the final person Evil Locke will need to win over and he will attempt to win him over by using Kate, Jacks ultimate weakness.
I think the show will build up to a Jack and Locke final confrontation. I think Desmond will have to convince Jack in the alt universe to kill John Locke during his inevitable operation (Locke will go to Jack to be ‘saved’ from his wheelchair, maybe so he can dance at his wedding! much like why Jack fixed Sarah). It will be the ultimate show of faith, to kill a man to save everyone,everything and not truly know why. I think that if Alternate Locke dies his spirit will cross over to the real time line and smoke monster Locke will eventually begin to be taken over by the real Locke. A little bit like at the end of The Matrix Revolutions when Neo allows himself to be taken over by Agent Smith. Lockes natural faith will imprison evil. He will become the cork. A few weeks ago we saw Smoke Locke echo real Locke by yelling ‘don’t tell me what I can’t do!’. The bridge between the two realities can bleed through. The fact that young Locke drew the smoke monster suggests to me these two are bonded. They are a part of each other.
I think this has all been part of Jacobs Loop to wipe out Evil once and for all. He’s planned for the alt reality and for Smokey to take on John Lockes image as his final form.