I think the correct term for flashes between universes is "bleeding through" (in homage to the recent rash of head gashes). I also believe that if both universes were real and were to merge, instead of nose bleeds, characters' heads would explode.
I also have come to a speculative conclusion of where the writers may be headed: that one of the universes does not exist; it is an illusion, a Room 23 construct, part of a long con. That is probably the sideways world.
I think the sideways world was a way to attempt to overwrite the real world to test candidates, to see if they could be fully mind controlled by Widmore. In the sideways world, Desmond's only purpose was to serve Widmore. He had no family life. He was all work. Complete loyalty. No questions asked. After the EM blast, those are the strong memories that are guiding Desmond, who now suddenly is following Widmore's orders.
The other candidates have too much "free will" or other baggage (like daddy issues) to be totally manipulated and controlled by the island keepers like Widmore.
Comic book science answered my question about Desmond's being EM-microwaved: Widmore was not "testing" him but actually "creating" a new Smoke Monster (DeSmokey) to take on the old one, Flocke.
I can see this projected sad ending: Desmond defeating Flocke in a smoke and lightning battle. But instead of keeping the false memories, Desmond sees flashes of his real life with Penny and his son. He rushes to the Hydra dock to find Widmore's sub already leaving the island. "Come back! Don't leave me here!" he screams.
From the deck, Widmore tells him he was the sacrifice the island demanded, that he can never leave the island, and that he could never see Penny or his son again.
Enraged, Desmond turns into a dark smoke monster and turns back into the jungle, ripping up trees along his path, just like the old Smokey in Season 1. He has become the new island Cerberus.
The whole island story would loop back on itself. This is how MIB "lost" his humanity, because he was turned into the island security system, a smoke monster, by Widmore's predecessor, Jacob. MIB was trapped on the island for eternity. Over time, he could not stand his plight and just wanted to end - - - cease to exist. Suicidal. The island does create a sense of madness in people.
Then over the final credits we could see Desmond wandering the beach and coming across the same Jacob-MIB beach scene, but this time when he says "You don't know how much I want to kill you," he would be speaking to Widmore.
