If the series climax was really about the Jacob-MIB struggle, we must examine the evidence of that alleged struggle:
1. Crazy Mother stole Jacob and his brother from their real mother just after child birth on the island.
2. Crazy Mother set down a rule that Jacob and his brother could not harm each other, ever.
3. Crazy Mother forbade them from making contact with the other people on the island (which were the remaining crew from the Roman ship that wrecked on the island with Jacob's mother on board).
4. Jacob's brother went to go live and work with the Romans. He decided that he wanted to leave the island and thought he found a way by digging pits to tap into the island's energy source.
5. Crazy Mother visited Jacob's brother and confronted him on his plans. Jacob's brother refused her demands to return to her camp.
6. Crazy Mother, a middle aged woman, destroyed the entire Roman camp, much in the way we would observe the smoke monster do to the barracks.
7. Jacob's brother was enraged by Crazy Mother's actions, so he confronted her and killed her with a knife.
8. Jacob vowed revenge on his brother, and did so by hurting him near the light cave stream. His bleeding body was washed into the "Heart of the Island" and a smoke monster rushed out - - - and Jacob would later find his brother's dead body in the jungle.
9. Jacob buried Crazy Mother and his brother in a cave ("Adam and Eve").
10. The smoke monster took the form of Jacob's brother (The Man in Black or MIB), but he could shape shift into many forms, including dead individuals.
11. The MIB smoke monster continued to follow Crazy Mother's rules that it could not harm or kill Jacob, so the smoke monster sought out other people to stab Jacob ( like Alpert and Ben). Albert was thwarted because he allowed Jacob to speak to him; Ben had a conversation with Jacob but somehow his stab wound was allegedly fatal.
12. Jacob apparently continued to follow the rule, trying to get other people to kill MIB, including Sayid, but his attempt was thwarted when he allowed MIB to speak to him.
13. Once Jacob was "dead," MIB took the form of John Locke (Flocke) and then tried to recruit people to kill Jacob's remaining candidates.
14. Once Jacob was "dead," the smoke monster convinced Desmond to "deactivate" the heart of the island (by uncorking it) which would free MIB and destroy the island.
15. Jack, who assumed the guardian role, returned to the heart of the island to rescue Desmond and to re-cork the island to stop its destruction.
16. When Jack replaced the stone in the light cave, MIB allegedly became a mortal human being, who would die at the hands of Jack and Kate.
So what were the magical rules that the two "brothers" had to play by?
It would appear that the stone cork in the light cave magically tethered MIB to the island. The cork also kept the island from destroying itself. This means that MIB/smoke monster was a prisoner on the island. That would also mean that Jacob, who could go off the island to recruit candidates, was not so trapped by the island cork. Logic would then assume that Jacob was not a smoke monster. However, we saw Jacob take other forms, such as his child self, before and after his death at the hands of Ben, just like a smoke monster. We also know that Jacob was immortal, living for centuries without aging.
When the cork was removed, the island began to destroy itself and allowed MIB to break the invisible chains. At this point, MIB was still a smoke monster. It was only after Jack re-corked the island did MIB actually became human (he could bleed). So the sole mechanism to give MIB human mortality would have been the removal then replacement of the stone cork in the light cave.
However, MIB continued to try to kill Jacob's candidates. So, it may have been another rule that if there was a island guardian (a jailor), even though the stone cork was removed, MIB still could not leave the island. But MIB had no rule against killing the candidates - - - he apparently did so with the Others, Dharma and some of the 815 survivors. (Some may say he may have only manipulated people to kill each other off.) Besides, Jacob broke the rule when he killed his brother so that pact was gone. (And probably true because Jacob hid in sacred places that the smoke monster could not get into such as the cabin protected by ash ring or the Tawawet statue.)
When did Jacob become immortal? It seems his immortality was granted to him when Crazy Mother gave him the island guardianship. And if immortality is part of the powers vested in the island guardian, then why did Jack die? Because he transferred his power to Hurley. But then, why did Hurley die?
That would mean that Hurley's death meant that he had to transfer the island guardianship to another person. But that begs the question. If the prisoner, the smoke monster was dead, why would there be a need for a guardian anymore? Unless, of course, there were other imprisoned smoke monsters on the island. And if there was no further reason to guard the island, why would anyone be left on it? Would not Hurley want to get the Others back to their families and their real homes?
The Jacob-MIB conflict still does not make clear, logical sense. If the smoke monster could not enter the light cave and tip over the stone cork to set itself free, then Jacob, being tired of his guardianship duties, could have just quit and left the smoke monster alone on the island. Since we were told only Jacob could bring people to the island, the smoke monster would be forever trapped on the island.
The puzzle pieces to Jacob still don't quite fit together. Was he a man or a smoke monster? Was he immortal or a magician? Was he truly killed or did he turn into a smoke monster trapped on the island as a result of his death?