ok, this may sound crazy but i believe the main central story of lost has been revealed and it all came together with the season 5 finale. ok, following on from the valenzetti equation in which mankind has a finate amount of time left until it destroys itself through various ways, here is the thoery of what lost is all about. Far into the future(i know its crazy but hear me out), mankind desperate not to extinguish itself tries to change one or more of the numbers in the equation. 2 sentient beings are created, these are jacob and his nemesis, who are able to judge and nurture mankind. With the whole history of mankind at their disposal they are sent back to ancient times to early civilisation. This is a test/experiment to change the violent naure of humans, Jacob and nemisis are machines, they read minds shapeshift and manipulate humans.
every hallucination on or off the island is nemesis, trying to tempt people to be weak and lazy but because of free will jacob isnt as involved. jacob brings people to the island ( starting from the earliest egyptians ) he chooses good people who he allows to live forever, eventually once the time has come around again where they were sent into the past, there will be generations of thousands of good humans on the island that jacob has chosen and were strong enough to resist nemesis, humanity may have a chance to continue to exist, and therefore changed one of the numbers in the valenzetti equation.
the end of lost will be this revelation by jacob to the people he has chosen like jack and kate, etc. they will stay on the island with all the other people he has chosen.