Here's my big Season 6 Theory:

Jacob and MIB represent the full potential / guiding force of the human race. They were created as the guardians or watchmen for humanity by some form of higher power, and The Island was created in order to give them privacy and closure from the rest of the world. Jacob and MIB were not created as inherently good or evil entities; they simply represented the balance that exists between life and death.

Jacob(white)was given power over guiding human beings and making sure they led civilized / moral lives, and MIB was given the power to use death as a check for anyone who abused the privelage of life. Furthermore, MIB (dark) was in charge of making sure those who led good lives transitioned smoothly into the next realm after they died. The higher power that created both of them ensured that they took a human form so they could interact with regular humans if they needed to. However, they were granted special powers in order to carry out their respective jobs, and both were given the gift of immortality. This allowed them to be the eternal watchmen. Yet, they could be killed by ordinary humans. This served as a check if they were ever to abuse their power as watchmen. It was made impossible for one to kill the other, though.

I suppose you could say my theory of Jacob and MIB is similair to the Christian view of Jesus -- they are both human and divine. Unfortunately, MIB and Jacob were both faillable due to their humanity -- for whatever reason, they became shortsighted. The two grew to disagree about the way humanity should grow, how it should be controlled, the good and bad aspects of its existence, etc. They began to bicker. Jacob believed in the promise of humanity, whereas the MIB grew cynnical.

This led to Jacob conducting an "experiment" where he somehow brought or lured human beings to The Island in order to prove their worth to MIB. Sadly, this experiment blew up in Jacob's face, and the people he brought to The Island failed the test in some way (most likely by slaughtering each other). Nontheless, Jacob continued to press forward to prove he was right. He conducted more tests / experiments.

Eventually, MIB got fed up when Jacob lured a ship called The Black Rock to the Island. A massive war ensued sometime after the ship arrived. MIB lost the battle along with a great deal of his power, and he was forced to take the form of the Black Smoke. Jacob still remained in his form, but he knew the balance was upset -- the two would never be able to perform their duties as watchmen again. The higher power that created them was absolutely disgusted with both of them and left our world forever. Jacob and MIB were stranded alone on The Island.

Richard Alpert, a slave from The Black Rock who was pivotal in MIB's defeat, was granted immortality by Jacob. He was to serve as a new kind of watchmen for humanity by organizing followers (The Others) in order to spread Jacob's message. While he was not allowed to serve as a leader, he was to choose the best of Jacob's followers in order to lead. Centuries later, a man named Ben Linus would usurp power from one of the leaders -- Charles Widmore. Though Jacob had faith in Ben, he eventually grew tired of his impatience and rash decisions. Therefore, he took away The Island's major gift to its residents: freedom from disease. Ben developed a tumor.

Jacob grew more and more concerned about the promise of humanity. He decided to conduct one final experiment / test. He was absolutely desperate, and he set in motion the events that would cause Oceanic Flight 815 to crash on The Island. Meanwhile, MIB (now fully evil and hell-bent on revenge) saw an opportunity for retribution.

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