I think what is going on is this.
The island does the ultimate reset and vomits MIB out as Smokey - the darkness is the opposite of the light.
In the episode we saw that the reason why MIB and Jacob are at polar extremes is that Jacob was willing to guard the island (with all the Oedipal complications that went with that decision) but MIB wanted to exploit the power of the island (even though he wanted to do so for probably morally neutral reasons). This faith vs. science argument has continued to be worked out through the Others (Jacob's followers) and their various enemies right down to their years spent fighting Dharma. The Losties got downloaded right in the middle of the argument right when the key players (Jacob and MIB) were at the zenith of their power.
It looks like they became opposites later, but why did mother dress them in black and white since they were young? Even the bracelets, Jacob's is white, his brother's is black.
To me it still looks like the brother wasn't expected and mother always knew that he was there to balance the scale, that he was science and would not just accept answers, that's why she loved him more, she knew he was doomed. She didn't want him to look for reasons, she hoped that he would not go looking for them if she told him that there was nothing across the sea, that the island was all there is, that they just came from her and she came from her mother, that people are always bad, but not them, they had a reason to live, a purpose.
She had no doubts about Jacob, the one who could not lie, the one that was always supposed to be the one, the one who would accept her answers and not question them or want a proof.
But Jacob is the one that leaves the island and observes the people, because he wants to know if mother is right. He doubts her words. And his brother is the one trapped on the island to protect it from people, that Jacob keeps bringing there to prove mother wrong.
