OK, here's my theory. Are we thinking along the same lines KoR-evo?
The Hanso Foundation located and set up the Island as a research centre, hiding and protecting it with an electro-magnetic field. They were conducting illegal tests using gene therapy with a view to eradicating illness and prolonging life. They needed sponsors and teamed up with the Widmore foundation, and possibly other wealthy individuals. They begin to make amazing discoveries - they unlock the secret to human DNA and learn not only how to create a new life, but to extend or regenerate an existing life. They begin to effectively 'clone' children with perfect DNA so in theory they should not get sick.
Through the Hanso Adoption Agency, mainly using Hanso staff or affiliates/sponsors, they 'place' the children with suitable parents. Some children may be placed through artificial insemination without the 'host' being aware of it Sun?). Hanso has medical facilities, which could have been visited by Claire or Hurley's Mother. Although I suspect Claire's ex-boyfriend may be part of this plot too, as he was terribly keen Claire should keep the child, and then left abruptly.
I think it is possible that Hanso couldn't live with what he was doing but Widmore wouldn't stop. This may be what caused the rift between the companies and also on the Island. Hanso couldn't shop Widmore without revealing his part in it. It's a bad plan that can't be changed...
I think the Island is now populated by the original Dharma/Hanso guys who started out with good intentions, and members of the created genetic family. Some of the inhabitants may be ex-military who were initially hired to protect the Island. We know Kelvin was in the military, and Ben was subjected to torture by Sayid yet didn't crack. The Other Others could be the Widmore guys. Ben's lot are the Good Guys. The animals were probably there as part of the genetic experiments. Maybe during the 'incident' some died and some escaped. Maybe the monster is a genetic mutation? Hmm.
The crash was arranged. The Losties were recalled when their Father's died, or possibly when one specific Father died (Christian?) Is this the price of regeneration? When the others refer to HIM, could they mean the man who played God and created them? The Others were confused when Michael claimed to be Walt's Dad and took blood from him didn't they??
I think the children are taken immediately by the Others (Hanso faction?) because they are still 'good'. The main Losties are being observed and tested first. The numbers could be a batch code for our Losties, or a specific part of their DNA sequence. Hence the feeling of the numbers being connected and pulled together in strands just before they got on the plane. Libby could be a facilitator, one of the people employed to manipulate the Losties lives. (The Fate theme). I think possibly Locke's tour and Rose's Honeymoon were both organised by the same travel agency. They are the only two who seem to understand what is going on, and were unsurprised by their sudden healing.
I think the reason for the Losties being recalled is for the nature -v- nurture experiment. Good genes don't necessarily make a good person. Does this mean the experiment is still going on, maybe to create the perfect world?
In summary, I think the Losties may be Foundies. Are they HOME? Was this always their destiny? Am I rambling??

I've only seen up to series 2, so some of this may have already been disproved in series 3.
Please feel free to rip this to shreds/discuss/Laugh..
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