Jacob is one step ahead by CHISCOT

OK – total theory here we go:

This is a conflict between two sides. On one side, I think we have Jacob, Ben and Widmore. I think these three are acting together, presumably under Jacob's leadership to entice the MIB (on the other side) into a trap.

So, in order of events:

Ben is made leader of the Others and MIB is led to believe Ben thinks Jacob lives in the cabin. Since MIB himself was resident in the cabin, MIB is therefore led to believe that Jacob has snubbed Ben by never appearing to him in person. Ben goes along with this –Jacob and he use Richard as a go-between. But Ben is being set-up, even then, as an agent that MIB can use to kill Jacob – since he is someone who should be expected to hold a grudge against Jacob (Ben of course, is fully in the know on this).

Widmore’s exile by Ben is then staged so he can be the man on the outside - and also to set up an apparent conflict between him and Ben. But really the whole exile is orchestrated for MIB's benefit.

Jacob, in the meantime in the outside world, has set up a karass of people to help him (see Cat's Cradle if you don't know what this is), and has engineered for his karass to be on flight 815, which he then engineers to crash on the island.

How the plane was crashed I don’t know. It is possible Widmore orchestrated for Desmond to be on the island and Jacob orchestrated the hatch and the numbers and so on, but it doesn’t really matter – the point is Widmore / Ben / Jacob, directly or indirectly, caused the plane to crash.
Widmore, from the outside, distracts attention from anyone looking for the real flight 815 by planting the "dummy" plane on the ocean floor.
Ben then leads "The Others" in a conflict with the new arrivals partly to sort out who can do what, test them and so on. Jacob may be letting some of this play through in genuine conflict so he can learn more about his "team" and who will be good leaders and so on – for example testing who will be the key people in the final showdown (presumably season 6). But in general I think the conflict between "The Others" and "The Losties" is a side-show.
Widmore then sends a tanker to capture Ben, but this conflict is a stunt designed to finalize Ben’s position as the outcast. The agreed to conclusion of this apparent conflict between Ben and Widmore is that Ben will leave the island as a bitter exile and therefore be set up finally as the potential tool for MIB to use to kill Jacob. That is why Ben is so shocked when Alex is killed, and why his visit to Widmore afterwards refers to "breaking the rules". It is possible Jacob and / or Widmore felt that going to this level was required for the trap to work, so MIB could use Alex as a tool (as he did in the temple) to "manipulate" Ben. Although Ben went along with this escalation, he still felt the need to exact personal revenge on Widmore. By the way, just because these two are on the same side does not mean they get along - there is plenty of evidence they do not. This is a side-show though.

Now Ben is outcast, the trap is sprung and MIB will feel he has his "agent" who he can turn to his side and use to kill Jacob.
MIB's question is how to turn Ben. He had previously been assuming the form of Christian Shepherd, but he knows the ideal form would be that of Locke. He knows this because as the smoke monster he has vetted and judged many of the people in Jacob's karass and has hand picked Locke for the role. I don't know if Jacob planned for Locke specifically to be the bait, or if he brought a range of people and figured one of them would measure up. Regardless, MIB chose Locke.

As Christian Shepherd (posing as Jacob, kind of) MIB then initiates the time jumps via the moving of the island, which ultimately is the chain of events that explains Locke becoming leader of "The Others" and therefore becomes someone Richard and Ben will implicitly trust. Locke is now established as the form MIB will use to manipulate his agent, Ben.

MIB then engineers what he thinks is a clever plan, whereby Christian tells Locke he has to leave the island to bring his friends back and that Locke will have to die. The real reason to do this is to manipulate Ben into killing Locke. I would guess he somehow manipulates Ben directly, but we have not seen what this involved yet. This ensures that Locke’s body is brought back to the island for him to occupy, and also that Ben will react with guilt and awe to his apparent resurrection and be more likely to do what he says.

As a side note, there seems to be a whole conflict off the island involving different sides. My guess is this is also engineered. One side is Ben (and Sayid and some other people Ben has recruited), being manipulated by MIB (or so MIB thinks), the other is Jacob / Widmore’s people, including Ilana. This ensures MIB really believes Ben is his agent. A complication of all of this is that the Losties do not trust Ben, and so Jacob has to directly and indirectly manipulate them into coming back (and bringing Locke’s body).

Once back on the island, MIB assumes Locke’s form and manipulates Ben into killing Jacob, as planned by Ben / Widmore / Jacob all along.
Jacob’s crew (including Ilana) then show up with Locke’s body to show the Others that Locke is not really Locke. It is very possible this body is not really Locke’s body since MIB is using that, and that the corpse is a wax-work or some replica made while Locke was in the funeral home. Clearing up this mis-understanding may be a minor plot arc / red herring of season 6.

The theory up to hear, I think is pretty well substantiated – from here on we enter the realm of pure speculation….
One thing I think is clear - Jughead did not explode. I suspect that having killed Jacob, MIB is going to try to destroy the island and it may be that Jughead plays a role in that (I am guessing Jacob may have orchestrated brining the US military to the island with the bomb, to that end –as bait for MIB to believe he now has the tools to destroy the island).

I suspect that Jacob also brought the Dharma initiative to the island, since their presence leads to the time travel device becoming accessible, that MIB would have needed that to create his loophole. It is also possible that the 1977 Losties were sent back by Jacob, to ensure Ben is shot and then saved – becoming “different” in a way that makes him the ideal candidate for his role as the bait in Jacob’s plan.
It is also possible that Faraday and Hawking are tools of Jacob – with Hawking being given a script of the future through Faraday’s notebook that lays out the plan for Widmore and Ben. It may be that since Jacob sent the Dharma initiative to the island (the Hanso family connection between the Black Rock and Dharma being more evidence of this), he made sure the plan was outlined to Faraday in Ann Arbor and fully scripted in the notebook in a way MIB could never discover (hence Hawking’s line about “the first time in a long time I haven’t known what was going to happen” after the final phase of the plan is put in motion).

How the cooperation between Ben and Eloise Hawking worked for Ben to bring the Losties back is not clear – but it must have been done in a way that MIB bought it.

I suspect the 1977 Losties will travel forward pretty soon in the new series so everyone is in the same place and time (perhaps Jacob does this as his last act – hence “they’re coming”) and that a fairly straightforward battle between them and MIB (and his followers if he has any) will ensue, resulting in the island being threatened with destruction by jughead, but in the end saved with MIB somehow destroyed and some resurrected form of Jacob living on.

I also suspect that the resolution for our Losties will be that they are able to somehow re-set and land in LAX as they would have done had the plane never crashed. I don’t know how this happens, but suspect it is some fall out of the end of the conflict on the island – perhaps a gift from Jacob. They then get to live out their lives from that point on, with all the knowledge and wisdom they have gained on the island.
This reset may not happen at the end of the series, but be shown intermittently throughout it – perhaps even from the start. It is initially a bit of a red herring since we are meant to think it happens because of jughead detonation by Juliet from the end of season 5.

The major real red herring, I think, is the numbers – I think this a side plot and that they will resurface in season 6, but since the producers originally included them as a plot device to get Hurley to meet Rousseau, I am not sure there is a lot more to them.
That’s it, all I got.