Ah, now we have it. The LOST writers are uniting the good vs. evil and time-travel streams into one story and it involves all of the principals having intersected before, during and after the plane crash, and Eloise Hawking (Daniel Faraday's mother and wife of Charles Widmore) seems to be the fulcrum upon which the whole time-travel element to the story pivots and will be resolved. She knows the answers and her consciousness seems to transcend the various time-streams of parallel lives we've been shown.
This Desmond-centric episode, Happily Ever After, finally brought back the sci-fi time-travel stuff, and as expected, returned Faraday to the equation.
So it looks like Mommy Eloise screwed up the time-stream originally somehow and she raised her son in one time-stream to skip music for science so he could try to right her wrong (something to do with the bomb probably), and she probably married Widmore because he had the money she needed to make things happen.
Widmore's daughter Penny and Desmond have some special time-equation properties also because they seem to factor into the events that led everyone to the island. Desmond must intersect with Penny in all time-streams and Desmond is impervious to huge electro-magnetic discharge as shown in Widmore's experiment early in the episode.
The whole subplot with Charlie was pretty good ... in this time-stream he's had a vision and seems to invite death by pushing limits on everything - hoping to have the revelatory moment he recounted to Desmond earlier. Charlie forces their car into a marina and Desmond has a flash of another time-stream also - he sees written on Charlie's hand "NOT PENNY'S BOAT" and then has visions of Penny and the two of them together.
Desmond is Widmore's favored errand boy/dealmaker in this time-stream and he tasks him with seeing his wife to break the bad news that Charlie's band won't be performing and this will disappoint her son (Faraday). She takes the news in stride and only turns into the predicted witch when Desmond mentions trying to find Penny. Eloise tells Desmond not to look for her to just leave it all alone.
Faraday overhears and takes Desmond aside and tells him he thinks they've lived other lives and are seeing flashes of these other lives and that he, Faraday, blew up a nuclear bomb in one of these other lives. Desmond looks at him like he's a wackadoodle until he says Penny is his half-sister and he can tell Desmond where to find her.
Cool back-and-forth between time-streams and story arcs this ep - well done. And at the end when a resistant Desmond is checked, found healthy, and released from the electro-magnetic experiment Widmore had subjected him to on the smaller island, he is a changed man. He wants his Penny back, and knows to go with the flow to get to her. Widmore told Desmond he'd have to make a great sacrifice, so likely that will end up being Penny (probably to set the time-streams right again).
Now I don't know how they are going to join up the supernatural with the science, but next ep is Hurley and his I see dead people, so maybe the ghosts will glue together the time-travel and good vs. evil for us. My worry is that the writers will give us a Schrödinger's cat scenario, whereby the nuclear bomb detonated on the island - with its weird magnetic properties opened a rift in time and now allows various time streams to co-exist with the island as an inersection point to all those people involved. My guess is the bomb serves the same role as the guy with the gun in the top Schrödinger Cat image - upsetting the balance.