I think the spinal tumor X-ray does a great job of explaining why they wanted Jack, and it's now pretty clear that they want "Sawyer" because of his skills as a con-man (to con who? for what reason?). What I'm wondering is "Why Kate?"
As for the others being good/bad, I don't think it's as cut and dry as that. I think the others, like the survivors, are both good and bad. Sun shot a woman to death, Ecco crushed two people's skulls, Sahid has tortured numerous characters, and both Sawyer and Kate have killed (or at least been responsible for killing) in the past. These are the good guys? Aside from kidnapping, sinking a raft, and playing mind games, what have the others done that's so bad? For all we know, they might be acting to ensure the health and safety of the folks they've taken... there's little indication they've actually put anyone in danger (compared to the relative safety of living on an island full of polar bears, tree-tossing smoke monsters, unstable dynamite, and crazy people.)
My guess about Desmond is that he could see the storm coming. I don't imagine he conjured lightning.