If you look at this entire show from the beginning, it's been kind of like Pirates of the Caribbean, in that characters are alwasy switching sides and forming temporary alliances and stabbing each other in the back. They seem to stick themselves with the people that have similar motives as them, but rarely trusting anyone. The only two conflicts that are actually deep-rooted and unchanging are Ben and Charles' quasi-mob war and Jacob and his nemesis' mysterious rivalry. I also noticed some other similarities between the two. I'm not postulating any theories or guesses; just hashing out some parallels:
1. It's obvious that there was some rule or law or boundary that prohibited MiB from killing Jacob. There was also a breif allusion to a seemingly similar rule between Ben and Charles. I apologize for not having the specific quote or episode - you guys probably know which one it is - but in the scene where Ben confronts Charles off-island in his office and tells him he's going to kill Penny, Charles asks "are you here to kill me?" and Ben responds "you know I can't do that." PROBABLY nothing to do with MiB's predicament, but an interesting line.
2. Both of these pairs of enemies have been leader figures. Well, we're not sure about MiB.
3. They both were once friends/allies, and now they loathe each other.
4. One figure (Jacob/Charles) wants to bring outsiders to the island, and the other (MiB/Ben) wants to keep them away
5. Both MiB and Ben are master manipulators
I know this may seem rather conceited, forced, and stupid. That's okay. No need to comment about that. But feel free to leave your agreements, disagreements, theories, speculations, and further parallels!