OK....This is a rambling attempt at making sense of all this:
If you look into the Hanso Fndn, their mission is all about improving life through the study of animals, electromagnetism, gene engineering, psychology, etc. The web site alludes to a number of projects that have gone wrong and that the company has covered-up to stay in the good graces of the authorities in the areas they operate. THIS island seems to have been the fusion of all of those experiments. At some point, something on the island went wrong (maybe the electromagnet started it, but we don't know for sure) and the Hanso Fndn bailed, leaving the surviors to fend for themselves.
The people that Hanso Fndn placed on the island initially (Others) were probably a mix of scientists and subjects from all backgrounds. When the "bad thing" happened, they must have all thought it was part of Hanso Fndn's plan and played along, living life as normal and creating a new cutlure/new set of rules day-by-day. Eventually they must have realized that help was not on the way....
Why did the plane crash on the island? Could be a number of things. Perhaps Hanso Fndn had been following the lives of those passengers and planned the crash so that they would fall on the island...To see how the "Others" would deal with these new inhabitants; each with their own personal drama.
Maybe the electromagnetic pulse (as seen on the computer readout at the end of the last show) was enough to rupture something within the plane or throw off its computer enough to cause it to crash? (The tail section seemed to sheer off during the descent, but did not seem to be the cause of the descent.) Maybe a plane didn't crashed the second time the EM pulse went off because...there was no plane close enough to the island at the time!
The final episode uncovers some secrets, but starts some new ones... We know the "others" are more advanced than they seem. Why the fake hatch and fake huts? And Walt told Michael they were "pretending."
We also know this, there are 8 hatches on the island, we've only really been in 2: The Swan & The Pearl. We also know the cave that the tail section people were staying in (Eko, Anna Lucia, etc..) was the entrance to the zoology hatch...Where all the weird animals come from.
But what was beyond the hatch that housed the baby room and medicine? What did it connect to?
I think next season we'll open up a number of new hatches and find out more assets on the island. It seems to me the Others still haven't found what they think they need to signal Hanso that they want to come home. Maybe they want Jack, Sawyer, and Kate to do their dirty work for them....
I also think the web site will lead us to the discovery of "the incident" that really occurred on the island by giving us more Hanso background.
