Apologies if this theory has been posted before (I think most theories are probably looping by this point...)
The magic box.
Way back in the early seasons of Lost (Season 3 I think) before the time travel element was apparent, we were introduced to the magic box idea. Benjamin Linus tempted and teased Locke by asking him "What if you could have whatever you wanted..."
At the time it just fell into the back of my head as another one of the unanswerable mysteries of the show, but upon hearing Flocke posing that same question to Sayid in last weeks episode I have rethought the idea (in relation to what we now know) and come up with a possible theory as to how the magic box operates.
Now, a lot of people are proposing that the island operates as a locking point for super position. That means that in every given possible alternate universe there will be differences, but the island is the one thing that is always constant.
If the island is apart from the diversion of alternating universes then the timeline on the island would always stay intact and hence the reason the characters still find themselves on the Island in season 6.
So how does this relate to the magic box?
Let's use Sayid as an example - he wants Naydia back but how can the island (or MIB) provide this for him?
What if the Island (or the corresponding science of the Island) could tap into all possible alternate realities to find a timeline where Naydia actually came to the Island? The forces of the Island would then converge the two realities to drag her to the independent reality of the current Island timeline.
What would this mean for her pre-existing reality?
Other people have suggested that Smokey is in fact a 4-dimensional being (as referenced from the book "Out of Nowhere") - that means he is a being that can occupy multiple realities and dimensions. This would fit with the ability to converge alternate timelines.
It is interesting that a lot of the themes in the show have revolved around characters joining sides, coming together and converging their own realities.
I'm not sure this will turn out to be the case but it's an interesting idea at least.