Sean Sheep, and probably many others, have speculated that MIB and Jacob are two parts of one person. Taking off with this idea, what if something happened long ago which split the man into two halves (one good, one bad?) Jacob's goal is to bring them back together again (balance) and MIB wants to be rid of Jacob.
This was directly symbolized by Jacob's scales (which were balanced when MIB found it). I can see this idea reflected in Christianity -- god allows evil to exist so that people have choices. If got wanted, he could eliminate evil, but he doesn't because it does have a purpose (to give us free will). Satan, on the other hand, would like to rule absolutely and would see no need for good.
I don't know how Jacob/MIB being "whole" again would affect the island, the people, or the world. I'm not even saying the above is where I think the show is going because I don't know WHAT to think. Fun to speculate though.
Side note: It keeps bugging me that Dogen said that Sayid's scale tipped "the wrong way". They always do that! He didn't say they tipped toward evil/dark, although he did say that Sayid had a "darkness" growing inside him. Anyone think Dogen may have been disappointed that Sayid was too good (or just not balanced)?