I am beginning to wonder who/what it was that little Ben saw when he had the vision of his mother, back in Season 2 (3?). That vision is what set him on the path to meet Richard and become a homicidal Other. We know Richard works for Jacob, but perhaps MIB enticed Ben, knowing how he'd turn out. MIB did after all use Ben to kill Jacob.

And the with the wheel not only lying beneath the Orchid station, but being functional beneath the station, I have to wonder whether that was found by Dharma, or found by Ben & co. after the purge. Because Ben knew how to use it. Perhaps thanks to MIB's teachings (which Ben mistook as lessons from Jacob)?

A final thought. I had wondered why Jacob didn't fight back or make any effort to defend himself when UnLocke brought Ben into his lair. Perhaps, like Mother, he was tired of being the guardian, and with his replacement candidates close at hand (They're coming), he was content to go (except of course that he keeps reappearing as a ghost). The funny thing, of course, is that for all of MIB's machinations, Jacob himself has left the Island numerous times.