I'm surprised nobody posted here in the L O S T  forum yet.  Here's my personal pet theory.

The experiments of Dharma still continue and the survivors, the others, everyone is still a part of it.  They were never in a plane crash as they never would have survived that kind of fall. They were placed on the island with the wreckage of an airplane, and here is the important part, with implanted false memories.  Every flashback that we have seen is false.  Locke could always walk, they've only told Kate she's a criminal, they've told Jack he's a hero. They wanted to find out if these people would act the way they really are or the way they are told that they are. 

I think it's the only thing that can possibly begin to explain things in the flashback's such as crossing paths, the reoccurrance of the numbers, whatever that was with Desmond, etc etc.

What's happening currently on the island?  Beats me.