On the island, Jacob has spent much of the last 30 years prepping the 815ers to be where they are now, but I think his cavern with the names/numbers suggests it's been more than just this lifetime. Much like Rousseau's distress call, this universe is on the latest of a seemingly endless loop, and just before it reaches the end and starts over again, both MiB and Jacob are trying to circumvent the inevitable, and break the loop once and for all. MiB has his plan, of course, but something tells me Jacob is a step or two ahead of him.
Narrowing down billions of people to a possible few dozen to the crash of 815, Jacob has everything (and everyone) in place for the end game. I believe this scenario has been played out every possible way except for the right way, and we're getting ready to see how it should end. Jacob and MiB have seen this play out so many times (dozens, thousands maybe) that while Jacob is still hopeful that it will "only end once," MiB is jaded, bored and ready to get the hell outta dodge. He no longer believes in anything bigger than himself, and on a show like LOST, that's totally the wrong way to think if you want to come out alive.
"Everything else is just progress" - When you have time on your side, as Jacob does, you have an eternity to find the constants, the needles in the haystack of all the variables out there, and Jacob has done just that with our six Losties that correspond with the Numbers. Knowing how important parents are in the show, I wouldn't be surprised if we find out Jacob even "touched" the parents of the 815ers, making sure they hooked up when/where they did to birth the children who would ultimately help break the loop. (Obviously you could even say he matched up grandparents and so on since the beginning of time, or at least at the beginning of the loop).
A couple side notes, I don't think Jacob had anything to do with keeping MiB "trapped." I think there's a lot larger force at work, hence the reason MiB is recruiting - to get a team together to fight this "war" we've been hearing about forever.
Also, I no longer think "The Incident" has anything to do with the ALT story. What really set it off for me was the lady working at the temp place in ALT is Hurley's fortune teller in the main story. I guess you could draw the conclusing that the fortune telling business isn't all that lurcrative and the temp place is her day job, but I doubt it. Next we see Ben Linus as a school teacher. At the time of "The Incident" in 1977, we know Ben was still on-island. I'm guessing the following didn't occur: Incedent - island sinking - Ben swimming away, thinking to himself, "man if I survive, I wanna become a history teacher."