I guess there are some serious divides between the camps on this series. The attempt to reconcile all the DHARMA-Military stuff to the Others mythical story, using logical reasoning will not end well.
Both storylines were prevalent in Jack, his journey from science to spiritual needed to create those conflicts so that he could form order from the chaos. But while these may come together at times, they can't both exist at the same time.
The supernatural meets reality is a staple of sci-fi. This show will go down in history as the most debated ever, for the first question is what was the story? Fantasy, Love, Spiritual, Drama, Comedy, Supernatural, Scientific, Relationship...............
My take, it was what it was, to each and every viewer who chose to devote time and reflection to the story that unfolded. I think the writers were successful in what many have tried before, to create a story that appeals to everyone at the same time. The parts one doesn't like can be skipped over without much loss to the story one wants to accept. Its also possible to view the show a 2nd or 3rd time and justifiable reach a different conclusion.
Now how many are capable of releasing their claim that they, and only they, are right, will separate the men from the boys.
Ambiguity to the end.