This is a little tongue-in-cheek but also somewhat plausible.
There have been a few theories that Jacob and MIB are the same being or entity split up - or that MIB is just one part of the Smoke Monster etc.
In Dragon Ball (Anime High-Five if you know what I'm on about!), a Namekian (alien race) tries to 'apply' for the role of Guardian of the Earth, but he cannot because he has some evil lodged deep within him. Therefore, he rids this evil by splitting himself into two seperate entities - one good, one evil - and he then becomes the Guardian and resides in the Lookout. Like Jacob, he is not revealed to the main character, Goku, until late on in the series.
This is the end of my parallel. Feeble, I know. But I was thinking a similar concept could apply to Jacob and MIB.
Of course, I'm not implying that Jacob is really a green alien, or that the producers would directly take an idea from a Japanese manga strip/ anime series. Just thought it was kind of interesting (more so if you're a hardcore Dragon Ball fan like I am!)