they both have special powers i guess u know jacob did meet jack,sawyer,john,kate etc b4 they ever arrived in the island and he even saved john lockhe when his father pushed him off the building
so both them guys have some sorta special powers
He met them because they time shifted into the 1950's where they ran into him.
So he knew they would be coming onto the island in the future and thus he left the Island and to go and meet them.
My guess, the Island being submerged in water will be the finale.
I think in the Island timeline, they are in 2003. And events will happen on the Island which will lead to the island being submerged.
As for the LA Timeline, it will show what will happen to them if the plane had never crashed and have a resolution for their stories.