Two central themes that have coursed through the veins of this show since Season one are Science vs. Fath. We should expect that these two themeatic juggernauts will have some bearing on the final outcome. And we can still see these being played out in the most recent episodes and even taking on the forms of actual characters on the show.
Jacob is blind faith, or the Avatar of blind faith. The Others (Templites, Hostiles, etc.) all follow Jacob blindly without answers. Rich Alpert is kept in the dark about the Candidates. Ben never met Jacob and always just blindly followed his orders. It is highly likely that even Dogen doesn't know exactly what is going on, just following lists tucked away in Anhks and not knowing why the water isn't clear.
MiB is science, or the Avatar of science. He wants to provide you with answers. He wants to convince you through logic and reason instead of asking you to believe in him. He wants to debunk blind faith, saying to Sawyer basically 'Exactly what are you supposed to believe in if you can't ask questions?' He wants you to be inquisitive and ask questions. Just look at what the ability to ask questions gotten us in the world today: We can fly planes and we can chat on the internet - one could say that we are progressing. When Jacob tells MiB, 'everything else is just progress', I think he was slapping MiB in the face - which is what peeved the MiB into wanting to kill Jacob. MiB was basically saying to Jacob that blindly following orders always leads corruption and death. Richard Alpert, a follower of blind faith, believes that road to scientific progress will lead to the death of everyone.
Jacob will not provide answers because he represents blind faith, the exact opposite of answers. If you have all the answers, then is it really faith that is guiding you or your own reasoing and logic? When Ben murders Jacob (he is murdering his own faith), he does so because he is asking for answers and Jacob can NOT give him answers because its not what he represents. 'What about me?'. You don't get answers becaus you are not allowed to ask questions. Such is the nature of blind faith.
Free Will is a huge part of this show. Free will is just the ability to choose for yourself. You have the choice to follow blindly without answers, or seek answers through evidence and explanations. Jacob clearly tells Ben before getting knifed, 'You have a choice'. You can put your faith in me, or you can seek answers. Ben asked for answers. The leader of the blind faith camp lost his faith - maybe that is part of the loophole.
This has run its course through the whole show. Jacob manipulated the Losties into getting on the plane and coming to the island. He also managed to get the Black Rock crashed there. I would bet that the MiB brought the Dharma Initiative there, since they were scientists. Why should we think that MiB has not been doing his own manuevering in the game he is playing with Jacob? Thinking about it this way, I am rooting for the MiB because I like getting answers.
I don't think the ultimate direction of the show is to say that Faith is good and Reason is bad. I think they are going to try and show that you really need to find a middle ground. If you side with Jacob or if you go with MiB, you are really limiting yourself and are really just putting yourself in a position to fight with the other side endlessly for all time since a resolution can't be had between the two. Free Will will play a huge impact on the main characters as the show ramps up to the end. I think the Others (Ben, Dogen, Jacob) have kept our main characters in the dark on purpose because when it comes time to make the final decision, Blind Faith or Knowledge, if they already know the answers, then it really isn't much of a decision, is it?
Wouldn't it be fun to watch the show from the beginning again and scream at the TV for them Not to ask questions becuase you don't want them to get the answers?