Here goes a theory or as I'd rather like to call it, viewpoint on S6, which I had last night as idea.
Basically I think that Jacob AND MiB together are comparable to the entity "Q" from Star Trek: TNG (and a bit in DS9 and VOY): http://en.wikipedia.org/wiki/Q_(Star_Trek)
It would take quite long to fully explain what or who Q is, but let's just say introductorily that Q is a, while not omnipotent, still quite powerful being which comes close to omnipotence when viewed from a human standing point.
What is much more interesting than what he is, though, is what he does.
In the pilot to Star Trek: TNG, Q puts humanity on trial on charges of being "savages" and only being capable of killing each other and others, and being no good.
In the pilot, Cpt. Picard and his crew get to solve a puzzle of sorts posed to them by Q to prove that humanity has a right to survive (see synopsis of http://en.wikipedia.org/wiki/Encounter_at_Farpoint), but they don't get told any clues let alone what the puzzle itself is.
Now each of them alone, Jacob or MiB, don't really seem like Q completely, but if you combine them both, they are very much alike Q who puts humanity on trial to prove they are good, but stays out of their way and lets them resolve the case themselves without major help, just a few nudges here and there maybe.
Q is also, like some currently think, inherently good nor evil, he just is, and while he sometimes mocks humanity or puts it into a problematic situation he is more like a force of nature than an evil entity by itself.
OK so, there is not much more to write, I think everyone who knows ST:TNG and Q, and has seen S6, will understand what I mean. If anyone has any questions, please post them in the comments.
Thank you for reading.