I am beginning to think that Jacob is not actually a force of "Good" on the Island, but is instead "Evil".
I would not be surprised that by the end of the series we find out that MIB/Smokie has all along been the good guy, and that Jacob is in fact the bad guy.
There are many clues throughout the episodes that leave me to believe this:
For example, when Ben takes Locke to Jacobs cabin for the first time, we are led to believe that Jacob is being held prisoner, and that he needs Locke to help him (Help Me!). We are also led to believe that the ash surrounding the cabin is there to either keep Jacob from escaping, or to keep some unknown evil entity (perhaps at that point in the story arc Smokie) from having access to Jacob.
We were supposed to think that Jacob was being held prisoner by an evil force such as MIB/Smokie. Well what if this was true, but the reason for Jacob being held prisoner, and ultimately being killed by Ben was because Jacob IS the dark force on the Island.
If you really think about it, its entirely plausible that the characters we have viewed as good, are in fact, bad!
This would explain the whole dilemma about us believing that Smokie at first protected the Temple. However, now because we have the "supposed" knowledge that MIB is Smokie, we are all questioning how something that at one time protected the temple, can now be the very thing the Others are trying to protect the temple from.
It would also explain the Sayid/Jacob theory. If Jacob has now taken over Sayids body, then it would explain why the Others in the temple want to "poison" Sayid to prevent the "infection".
If you really think about Jacob being an evil entity on the Island, alot of the other things we have known about the Island and the fight between MIB and Jacob make sense.
After all, things are not always what they seem on Lost