Okay, I'll give you Karl (and I basically contradicted myself by saying the Others couldn't have children and then saying, duh, he was born on the island! whoops). But the submarine--come on. Someone built a submarine beacon that appears to lead back to what Dharma built. I really don't think I'm "assuming far too much" to say, hey, maybe the submarine belonged to Dharma! There's no reason to hypothesize the existence of yet another bunch of people who were lured to the island.
I figured Karl was being kept prisoner because he and Alex aren't allowed to be together, and he tried to escape to be with her. Why they aren't allowed to be a couple seems to me like a genuine mystery, as in, something the writers will need to address.
Anyway, I'm clearly missing the point of the list, so I'll duck out. Sorry if I'm being too much of a dick.
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