While the Oceanic Six preparing to return to the island is the biggest piece of the "Three Years Later" subplot, they weren't the only ones to get off the island. Several characters are off who presumably still have something important to add to the story (Walt). So they bench the Oceanic Six in favor of the story of Desmond's quest to locate Daniel's mother while Daniel tries to help The Others with their bomb situation on the island 53 years previous.
Since he was never seen in flash forwards, Desmond's post rescue life was unknown, here it's shown that Desmond and Penny got married and had a child, named Charlie after the Lostie who made their reunion possible. Of course the other Charlie is Penny's father, the reason why they are in hiding on the house boat. With the time jumps, some are guessing that Charlie is a young Charles Widmore. While it's great that Lost has people theorizing about what's going on, this theory is too much. Penny would be her own granddaughter (not to mention the continually degrading DNA with the circular nature of this time travel)! Even if they softened it by having her be adopted, it's still a bit creepy.
With Desmond and Penny together and two more seasons on the clock, many viewers are rightfully worried that this relationship is going to end in tragedy like almost every other coupling on this show. Some are waiting for the "trouble in paradise" that comes whenever a couple gets together mid series and they need something to replace the tension. There were hints of that when Penny chimed in that Scotland was also where Desmond broke her heart, but it's not much further than that.
Also, there could have been tension with Desmond's mission, but Penny was easily sold on the idea of doing something Desmond was told several years earlier that he just happened to remember after waking up. There was the possibility of her thinking it was a dream or questioning it's legitimacy, but since we know it happened, that wasn't explored.
Although Desmond insists that he will never return to the island, his path to Daniel's mother, in LA with the Oceanic Six, will lead him there eventually. Now what does that mean for this relationship? A lot of people assume that Penny will have to die for him to come back, but how would they deal with that besides have him grieve and pursue revenge like Sayid? Or would they go with his original predicament being trapped on the island away from the woman he loves? She and Charlie can always come with him, but what implications would that have (besides the incest that was mentioned earlier)?
Desmond is also in an interesting place as he has overcome his major flaw, his cowardice. The best example is storming into Widmore's office unannounced, demanding information about Daniel's mother and not even speaking of Penny's condition. He couldn't do such a thing before. Desmond's life, hiding aside, isn't so bad. He gets to spend his time with the love of his life and their child, and Penny has more than enough funds to keep things stable. However, considering Desmond is a central character in the story, all these right steps may be sacrificed for him when he returns to finish his business with the island.
In the big confrontation at Widmore's office, Widmore shows a brief moment of fear and concern over his daughter. Ben put her in his cross hairs as retribution for what happened to Alex, and Widmore knows that Ben has the resources to fulfill his promise. Widmore may be aware that Ben is in LA, and having Desmond go there would put Penny at risk. For a man who seems to be in control like Widmore is, expressing any fear is worth noting.
Despite being officially a Desmond episode, we learn much more about Daniel via Desmond's search. Perhaps encouraged by what he saw in Desmond in 1996, Daniel took his research to an extreme, leaving Theresa in a catatonic state. He splits for America and Oxford pretends he never existed despite not throwing away his things. The big reveal was that Widmore was funding Daniel's research and took care of Theresa, showing temporal displacement can be relieved medically, after Daniel left. It's another interesting link tying these two characters together.
53 years earlier, the castaways are trimmed down to six following the attack from the people revealed to be the 1954 Others. Of course the ageless Richard is there, and it's common knowledge among his people that he is "old". Unlike prior times, he comes off as the leader with Ellie and a 17-year-old Charles Widmore as lieutenants. Alpert said leaders were trained young, but it's inferable from Ben's flashbacks that he really became the leader in his 30s. So at this point they were still some time from being fully anointed forces.
Widmore being one of The Others 50 years before the crash isn't surprising, but a good development. He had to have a back story with the island between his obsession finding the island and his rivalry with Ben. Obviously Ben's not around in 1954, but here we see that he was cocky underestimating Locke and such an attitude would breed a sense of entitlement when told he couldn't have something he wanted.
The Others mistake the Island Six (as they'll be known) as US soldiers. They'd been combating those intending to detonate the eponymous bomb on the island, and they believe that they are a part of this, even with Miles and Charlotte on the team. The bomb, besides being a classic device, also ties into one of Lost's major influences, The Stand, where a bomb plays a key role in the climax.
To convince The Others that he's intent on helping them with the bomb, Daniel tells Richard he's in love with Charlotte, which is more affecting than most of the shipper stuff. Although it can be hard to sympathize with Charlotte most of the time, Daniel's puppy love is definitely relatable.
Sawyer's scolding Daniel for telling Ellie they were from the future could mark a major sea change for the Losties. In the beginning they were the outsiders and The Others were the ones withholding the secrets of the island. With three plus months (give or take with time jumps) on the island, they've learned a lot about what's happening. Some have theorized the Losties will wind up the series as the new Others, so a moment like this can reinforce that claim.
It's interesting that Richard's attempts to reach Locke before the crash were because Locke told him to when he was in 1954. There are a lot of questions that come out of that, but considering the no paradox rule the producers, Richard was going to be there when he was a newborn and kid somehow. It may explain the test Richard gave Locke as a boy; instead of it connecting to the idea of reincarnation since the Dalai Lama takes a similar test when being chosen, the item literally belonged (or will belong) to the tested.
Like a lot of Lost, this introduces a lot of elements that will likely be big in the future, specifically the bomb, so it helps to rewatch after seeing the whole season. With the narrative all over the place, the writers are doing a good job keeping it together. It's no where near Desmond's best episode, but it has some points that may be important in the end.