My theory on why certain things don't add up(or are confusing to put together) is that originally the writers didn't expect the show to do as good as it did, they thought it would probably end in one or two seasons. They have always had the same plan on how to end the show, only what it turned out to mean for the rest of the show was different then originally interned.
What I am trying to say is that originally, the island was meant to be the purgatory (Limbo or what ever). However, after 5 seasons of expanded mythology and with the oceanic six leaving the island and coming back, the writers thought it would be cheating to the audiences to explain everything as purgatory. So instead they created the flash sideways as a way to still end the show in the same way they had always planned, while allowing the island and all that happened on the show to remain in reality. (or for some people, to matter)
So for the first two seasons or maybe just the first(because by the second the writers were already saying that everything could be explained by science) the island was still purgatory. All of the mysterious things didn't really matter because they were not actually in reality and were just tools for the survivors to find redemption. Those who came to the island were troubled in their past lives as jacob said(although jacob as we know him did not exist back then). Then they found redemption on the island and were accepting who they were. If the show was to end then, they would have all moved on from the island. However, rating were so good that the show had to keep going and the writers had to mix it up and expand on the mythology.
Now since the show didn't end in season 1 and continued on we got all the wonderful mythology. I see now what the writers meant when they said we wanted to put it in but it just didn't go with the story we were trying to tell. The thing is they were telling the story of this group of people and they only had so much time to tell their stories.
Of course there were so many other stories they could have told in this universe, such as all the people before jacob that built the temple and how they found the island. How hurly and Ben's rule of the island went. What was going on with Walt, miles, desmond and hurly. Basically this is where the majority of our unanswered questions come from. But you have to realize the answers are all there, in a way, with a little imagination.
When they switched from the island being purgatory, to the island being in reality it changed the world that lost was based in. It then became a world where there are pockets of special energy or what ever you want to call it that cause strange things to happen. The island is a hot spot of this energy and has special properties. It only make sense that other strange things could happen in this world such as Hurly being able to talk to the dead or Walt being well, weird. (my guess is these people have been affected by the energy and it changes them) They have said that they didn't want to explain too much like they did in star wars with the force(Midi-chlorians) and Im ok with that. Just take all you know form lost and use your imagination a little.
I think that through the contrasting of ideas when looking at season 1 and maybe 2 as purgatory to understand where they were going back then and then accepting what the show truly turned out to be is the best way to get closure on the left over questions.
I loved the show lost over the past six years like so many of you and was so worried that I would be disappointed by the finale. Even though I feel like they might have stretched the shows true purpose through the last couple seasons (expanding on the mythology that only led to more questions)... I feel that it was always a great ride and the Finale for me was the peak of the show. Truly a great series.