Ok, so this is just a quick little theory I had after rewatching the premier episode.
It would seem to me that these two universes that we are seeing are bleeding through to each other. This was first brought to my mind when we see Jack's neck bleeding on the airplane.
I have thought that the deleted scene in season 5 when Faraday explains to Jack that if you try to throw little rocks into a stream there is no effect, however if you throw a huge boulder (like a hydrogen bomb) there is an effect.
Now think about this literally. Imagine a stream of water being interrupted by a large boulder, what would happen? The water would split apart into two streams and one would go around one side and one the other.
However, when the water is passed the boulder what would happen? it would come crashing back together into one constant stream.
Thinking about the two universes we are seeing like this makes so much sense to me and I wonder if they took that scene out because it gave too much away.
Back to my theory that these two universes are bleeding through to each other, what made me really think about this was that last conversation between Locke and Jack. Locke seems to have accepted the fact that he will never walk again and that his condition is irreversible. And what does Jack say to this? "Nothing is irreversible"
This made me think that in this universe Jack is going to attempt to fix Locke's disability and by now I am sure you can see where I am going with this.
What if he does in fact fix Locke in this universe and he can walk again. Could this be the reason Locke is able to walk in the other universe when the plane crashes on the island? The two universes are and have bleeding through to each other sporadically and we have unknowingly seen this taking place all throughout the first 5 seasons of this show. I know there are discrepancies with the timeline here but as we see there are HUGE discrepancies with everything we are seeing in this other universe, Des is on the plane and married, only one bottle for Jack, Jack's long hair etc. etc.
Just a thought