I'm calling it now: Faraday will cause the Incident.
Faraday is looking for a way to save Charlotte. He knows that he can't tell young Charlotte to leave the Island and never come back, since that will eventually result in her coming back anyway and dying. But not telling her to leave will result in her dying in the Purge. So he must find another way.
This season's opening scene made it pretty clear Faraday is going to mess with time in the Orchid. However, I believe his path will eventually lead to the Swan.
Faraday knows Desmond is special, that the rules don't apply to him. He will want to reproduce the same effect on himself, so that he can cheat destiny. It shouldn't be hard for him to figure out that the reason for Desmond's specialness is the radiation he underwent by turning the Swan's failsafe key. Thus, Faraday will willingly cause the Incident so that the same happens to him.
Whether he will actually manage to change things, that's another matter. I doubt it.
I also believe this to be the reason why Faraday was crying when he saw the news of Oceanic 815's wreckage being found at the bottom of the ocean. Being radiated by the electromagnetism unstuck his consciousness in time, resulting in him feeling emotions associated with 815 (Charlotte dying) even when he hasn't experienced those yet. Much like Desmond didn't remember his meeting with Faraday at the hatch until many years later.
And it could explain why Eloise Hawking appeared so cold when Desmond mentioned her son. She is trying to maintain/protect the timeline from being meddled with, and thus he opposed everything she stands for.