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I have a new theory regarding Jacob's "Touch".
At the end of S5, we were led to believe Jacob's Touch (S5x16-17 "The Incident") occurs prior to the original timeline. That is to say, it preceded Oceanic flight 815 and began a chain of events leading them to crash on the island.
Theory: What if Jacob's touch created the alternate timeline.
In this new theory, Jacob touched the Losties forever changing their lives but it actually created a new timeline. Why? Because "it only ends once and everything else is progress". Jacob realizes the island needs to be destroyed to end the perpetual loop and for progress to be made. In addition, it can end the life of the Nemesis, rid the world of the island and bring peace to the Losties for good.
After all, sacrifice is an underlying theme of Lost and what greater sacrifice is there in the show than Jacob sacrificing the island to finally end the loop. Maybe that's why Jacob was resigned to dying. The original timeline, I believe, now represents the continuation of the loop, but that timeline will eventually be destroyed (possibly by Jacob, the Nemesis or Losties) leaving only the alternate timeline. Not sure how it will happen, however, as there is much to be revealed over the course of S6.