For a show that so heavily emphasizes duality, we've had a strange dearth of twins. A few sibling sets, but no actual twins. Now, I have absolutely no proof of this theory (just my mad ravings), but I'm going to posit that Daniel and Desmond are actually fraternal twins. (With the references to Esau/Jacob, I'm sure we'll find out two of our characters are actually twins in season 6---I think this pairing is the most likely.)
Look at the Biblical story of the fraternal twins Esau and Jacob. Esau, the elder, is a hunter, a 'manly man,' and his father's favorite, whereas Jacob, the younger, is the family brainiac and is favored by his mother. Here, Desmond echoes Esau and Daniel echoes Jacob: Desmond, the former soldier, the sailor, vs Daniel, the physics genius.
Daniel was raised by Eloise and he resembles her in a couple of ways. Physically, he's kind of scrawny; Eloise (especially teenage Eloise) is also on the small side. Daniel is the great physicist; we saw Eloise formulating equations in the Lamp Post, a possible hint that Daniel inherited his science aptitude from her. We know that Charles Widmore is Daniel's father, but for the life of me, I can't find any similarities between the two.
But there are a ton of similarities between Desmond and Charles. Physically, they're built the same: same athletic build, same curly hair. (The hair has to be a clue to something---Eloise remarks on Charlie Hume's curly hair, comparing it to Desmond's, and the actor who plays young Charles Widmore went to the trouble of wearing a curly wig.) Desmond was once a soldier; we first see teenage Widmore dressed in a military uniform. They both seemingly ended up with women who were 'higher up' than themselves: Penelope is far wealthier than Desmond, and Eloise was Charles's leader. Furthermore, notice the way middle-aged Charles is dressed on the Island, and compare it to the way Desmond dresses when he confronts Charles about Eloise's address: they're dressed almost identically.
Of course, we'd have to assume Penelope's adopted. Which actually makes sense, when you think about it: the Charles Widmore we saw on the Island was passionately against the idea of interacting with 'outsiders.' It seems strange that he'd have an affair with an outsider off-island when he's so 'Other-centric.' Penelope could be the child of another of the Hostiles; she could be a kidnapped child of Dharma. With the Widmore/Ben parallels, it might make sense that Widmore's daughter was adopted just as Ben's daughter was adopted.
It's certainly possible that Penelope only chose Desmond because of his unconscious resemblance to her father, but since she and Charles aren't close, it would be odd for her to do so.
How would Desmond get separated from his parents? Suppose Eloise gives birth on the Island. (We don't know for sure that The Incident was the initial cause of the birth problems---in fact, it makes sense for that to be a relatively recent problem, as the Others only started investigating the problem in the '90s.) She takes Daniel off the Island, leaving Desmond with Charles.
Well, Dharma thinks the Hostiles kidnapped Ben. Eventually they're going to come looking for him. And since both sides would assume the truce to be broken, hostilities would probably re-start. If Dharma attacked the Hostiles' camp in a later year, they might have grabbed young Desmond and shipped him off to Scotland. (Yet another child kidnapped to 'give him a better life'---here, a 'better life' than that of the savage Hostiles). Widmore starts leaving the Island to search for his son, and he is eventually exiled. He only finds Desmond when Desmond gets together with Penelope, and by that point, he knows he has to manipulate his son onto the Island.
That's why Naomi had Desmond's picture---she was supposed to make sure Keamey didn't kill him.
This is, of course, just a theory. I just think it's strange that, on a show like this, we've never seen either of Desmond's parents. Instead, Desmond's daddy issues are centered squarely around Charles Widmore; plus, Desmond keeps meeting with Eloise and Daniel, and Desmond was important enough to Daniel to be the latter's constant. Jughead makes it clear that Widmore doesn't hate Desmond. I'm wondering if maybe the writers have hidden the truth right in front of us.