I would like to add my own theory that the well is actually the fountain of youth and mother/Jacob are the protectors of the Fountain of Youth, which has granted them extraordinary longevity and as mother explained to jacob that many people have searched for her well and have failed so far.
Eternal youth is a gift frequently sought in myth and legend by explorers(this is possibly widmores search) but if the balance of life and death is upset it may bring about the end of the world as per the running theme of the weighing scales in previous episodes’.
And also with this gift there is a price to pay, to be the guardian of the well maybe a fate worse than death actually not being able to die and to live forever while all your loved ones age and die (unless you find a replacement to release you from your bonds).
Also there may be a possible plot twist explanation about jacob which may coincide with the theme of the weighing scales also it is that jacob & brother/MIB/smokie are one in the same person(split personality)we only see his brother from jacobs point of view and mother may know about this and is using it to her advantage(she knocked him unconscious in the well by grabbing his head and jacob may have killed the settlers and filled in the well to prevent his bad side from leaving the island .
As mother explained on the beach “you’re special”and she explained that she fixed it so that he and the nameless brother could not harm each other and when jacob asked mother why she favors his brother she never really answers him.
Is it an internal battle within Jacob good v evil, was it actually Jacob that killed all the settlers on the island and also his mother and then proceeded to have a psychotic split and cast his evil side down the well out of remorse for what he had done?.
This may have created a paradox within the island (it cannot kill the nameless brother without killing Jacob as they may both be the same person /split personality-if there is no guardian there is no protection for the island)
Maybe Jacob is now trying to fix the damage he has done because this may have affected the balance of the island and has set in motion a complex remedy using the OTHERS to bring back his other half (desmond pushing the switch to relieve the pressure within the islands inner turmoil ) .
Well that is my theory at the moment, guessing the outcome has been most of the fun In watching lost.