I believe that not only is L O S T a battle between the forces of good and evil, I believe it’s a battle of Science vs Faith.

Jacob brings people to the Island in an attempt to prove MIB wrong, but doesn’t directly interfere, you could say he places his faith in these candidates to do the right thing.

We know very little about MIB, but I believe the reason he turns into a pillar of smoke is due to some ancient science experiment gone wrong, hence the weird mechanical sounds whenever Smokey moves.

This would tie in nicely with the Ancient Egypt theme that has been ever present, as the Ancient Egyptians were not only people of faith, but also (supposedly) technologically advanced, years before their times.

So essentially what we’re seeing is a battle between
good and evil
faith and science
Jacob and MIB

and possibly…..

Jack and Locke – with Jack being the new man of faith and ultimate replacement for Jacob, and Locke/MIB the man of ancient science trapped on our quant little Island

Discuss

Honestly, I think the whole "science vs. faith" thing is more of a thematic element than a central part of the story.

I think the show is very aware that seemingly exclusive paths will find a way to cross each other, or balance themselves out - and in the end, they're both part of a single whole. A good real-world example of this is a scientist who is devoted to a theistic religion.

This fits with Jack becoming who he is. He hasn't completely taken up Locke's old role - because he's still Jack. He's still the doctor. He's still grounded in direct reality - what he can see and touch. It's just that he's seen and touched time travel and numerous other things to expand his views. But his central character is all still there.

Not to digress on Jack too much, but if the writers are (still) good, this final arc for Jack will bring him full-circle. When the "big answer" is revealed, he'll be enraged at all the illusions he had finally given into in the last few seasons.