My theory:
The Mother was the keeper of the light. It was her job to protect it from going out by way of people finding it and trying to take it. She was tired, no telling how long she had been doing it. The "Keeper" is endowed with certain powers. (Stick with me on this) The powers are the ability to cause things to happen, ships and planes to crash, immortality, and best of all the ability to become the smoke monster and kick a$$. Mom is tired and senses the pregnant woman passing on a ship. She makes a storm finds the woman adn takes care of her. She has a bond with the baby, she senses that it is special. Only problem is Spidy sense powers don't pick up on the second baby. MIB is the special one destined to become the keeper of the light but low and behold two babies pop out instead of one. She raises them and intends for MIB to be the one, but because he is special he sees his birth Mother and is corupted away from Mom. That leaves only Jacob so she turns the reins over to him. My explaination of Mom and her time on the island is derived from reading to many vampire books. Ann Rice's Interview with a Vampire series of books explores the idea that they can never find a vampire more than 4 or 5 hundred years old even though they know vampires have been around much longer. Lestat explains that the life becomes so lonley and unfulfilling that at some point the Vampire wants to die. Translation: immortality aint all that is cracked up to be. Same thing happens to Mom. Obviously she doesn't age in the 40 plus years we saw in the show. She thanks MIB for killing her because she gets to rest, she is free.
However her exit from this world creates a dilema, in that in the aftermath Jacob gets the power and immortality but because of his actions with his brother MIB winds up with the smoke power. This is not supposed to be the way it works. One person is supposed to hold all the power. Now it's split powers with one who wants to leave and both limited by the "rules" that Mom created for them when she still had the power. Remember Jacob gave Richard immortality and Mom gave it to MIB when she said you will never have to worry about death. She gave it to Jacob when he drank the wine and turned her duties over to him. So MIB is not Mom's son because he is dead, he is just the form smokeky took when a body floated by, the same way he took Lockes form when it returned to the island.
So now I am trying to not confuse the original MIB's wanting to leave the island (your not my Mother, those are my people, etc.) with the reason Smokey wants to leave the island, ( to inflict evil on the world, be free)
That's what I am thinking today but then again it's Lost wer'e talking about so it can change tomorrow.