Ok.. here's what I am thinking about so far...

first ~ the island IS a living entity, or thing, and does not have the limitations of mere mortals like us.. E.G. Time, science... it's more of a magical and acient alien like monster in itself...

second ~ dharma is not in complete control of what is going on.. that is why they seem to be running under the gun... here are some ideas... Dharma brought the people here because they needed test subjects, or people who have no idea about what dharma is trying to do. Dharma needs these people to try and manipulate and control the island.. but the island has a will of it's own as well... and maybe has it's own intentions of stopping dharma, by using the survivors. what I mean is ... dharma uses the island to bring people to the island... and the island uses Dharma to do the same.

thirdly ~ The island is manipulating survivors and pushing them in directions to stop dharma... l.E. John Locke... the hatch... the monster... ETC.

fourth ~ The other others are the descendants of the black rock... they are more intuned with the ISLAND. I think when we saw people and children with a teddy bear walking through the jungle that was them... oh... and they are all infected... with this discease... but they have lived with it for so long... the discease my really be something of a curse... brought on by the life blood of the island... which leads to my next set of theories...

fifthly ~ Henry Gale is "he" and he is has taken it upon himself to finish the job that ethan was supposed to accomplish... and he is kind of a Kaiser Soze because he does put a little truth..

sixthly ~ Dharma is Extracting Non-metallic material for their own means and design... Henry was talking about owning a non-metallic mineral company or something to that fact.. and I think that the black swan bunker has to with that.. and that the numbers have to do with Atomic Numbers of the elements... and they are extracting those elements from the island... I don't know if this makes sense to many...

seven ~ The minerals being extracted from the island are the life blood of the island entity.

that's all I got so far... I just believe it's more than one thing... but simpler than what I think is going on... their are two systems of power here...

science vs. the occult.