After the thought-provoking events of the previous episode, it makes sense for the writers to step back a bit and prepare for the finale. This actually feels more like the first hour of the finale than an episode in and of itself, but that's largely the effect of the serialized nature of the series.
The entire season has been split between the events in the past and the events in 2007. The vast majority of the story has been set in the time of the Dharma Initiative, however, which suggests that the events in 2007 are mostly setting up the situation for the sixth and final season. With all the foreshadowing of a final conflict over custody of the island coming in the final season, it seems reasonable to assume that Daniel's recent theory was wrong and Jack's plan will fail.
Jack is currently on an interesting journey, one that roughly parallels Locke's journey towards the end of the second season. Jack is trying to find meaning in everything that has happened, because it has defied his season of rational order. Because it appears that Locke was right about his own destiny, Jack has come to the conclusion that they all have a destiny to fulfill, and he's trying to find one that can restore his former certainty.
The irony is that Jack, like Locke before him, is not truly changing. Just as Locke was still hung up on his own expectations of destiny and self-importance, haunted by the past, when he tried to take control of event in the Swan Station at the end of the second season, Jack is only changing the manner in which he tries to take control over a situation. He talks about destiny, but he's more interested in denying the last three years of his life than learning from them. In terms of the redemptive theme of the series, Jack still hasn't made the turn.
With regards to the rest of the Oceanic Tribe, the situation at the Dharma Initiative is rapidly spiraling out of control. It's a bit surprising that it took so long for someone to use Juliet against Sawyer, once it was clear he wouldn't talk. It's one of those standard interrogation techniques (hurt a loved one to convince someone with a stiff upper lip to talk), and Horace wasn't above questionable methods with Sayid. It's also surprising that they agreed to let Sawyer and Juliet leave on the sub, and didn't bring up the fact that Sawyer, Juliet, and the rest of their friends just showed up one day, three years earlier!
Similarly, Pierre Chang's decision to believe Daniel's story was a little convenient, since there was nothing concrete to base that decision on. Questioning Hurley was a smart move, and one of the more amusing moments of the episode, but it still seemed a bit too smooth a process. That said, it does close the loop on the question of when Miles and Charlotte left the island. It's not entirely clear how Kate convinced Radzinsky or Horace to put her on the sub as well, or why Miles, Jin, and Hurley didn't attempt the same, but there wasn't necessarily time to cover those details.
It's good to see more of the tunnels under the island, dating back to ancient times. One might assume that this is how Cerberus gets around, since it's source is also underground. Richard specifically mentions that there is a way to get Jughead out of the tunnels, but it's not the way they came. It could be that they don't get the bomb anywhere near the site of the Swan Station, and instead, at the time of "the incident", it is closer to a portion of the tunnels close to where the statue once stood. That could, in turn, link to Ilana and Bram's gambit in 2007. (Radzinsky's decision not to take the warnings seriously could, in turn, explain why he chose to man the Swan Station for so long, and what ultimately drove him to suicide.)
The events in 2007 hint at some possibilities for the direction of the sixth season. Clearly, Locke's attempt to find Jacob and kill him is a big deal. This seems like it comes out of left field, but that's not necessarily the case. In "The Man Behind the Curtain", in the third season, Jacob specifically asks John to "help him". One possible implication is that Jacob serves the will of the island, but no longer willingly. He may do what is necessary for the good of the island, but he may have been doing so for so long that dying and passing that mantle to Locke may be his personal design.
The fact that Ben never actually spoke to Jacob is therefore an important clue. Ben was never supposed to be the leader of the Others; he took on that mantle because Locke wasn't ready. The island chose Locke, by whatever means it might do so. It's a fair bet that Charles Widmore never spoke to Jacob either, leaving only Richard as someone who has supposedly talked to Jacob or knows Jacob.
The devotion to Jacob, then, is akin to devotion to a legend. It touches on the various "Wizard of Oz" references associated with the Others. What if there is no Jacob? Or, rather, Jacob is not what he appears to be? The ship in a bottle at the beginning of the episode seems like an intentional reference to the Black Rock. Could Jacob and Richard have arrived on the island on the Black Rock, with Jacob chosen by the island at that time to "interface" with whatever was already there, dating back to ancient times?
After all, the Others all seem to come from a roughly modern time, which implies that they were absorbed into an existing population. That's not a new observation, but it's been an open question of when the "original" population arrived. It could have been the Black Rock (which would, in turn, provide a connection to Hanso and the Dharma Initiative), and then a series of subsequent arrivals of smaller populations. After all, there's no indication that people didn't come across the island between the late 1800s and 1954.
Touching back on some early theories (from the reviews for the first season episodes), the island may be inhabited by a non-corporeal entity, and that entity may be acting through Jacob. It may only be able to act through the bodies of the dead. If Jacob died when the Black Rock came to ground on the island, and then was resurrected by some ancient consciousness that is "the island", that could explain why he is so revered. Since Cerberus is already something of a non-corporeal entity, it's not completely off the beaten path. That would explain the "modern" look of the Others, while still preserving the implied ties to the ancient past.
It may even explain why Richard is worried about Locke's intentions. Richard may not be the leader, but he certainly holds power as one who does appear to know Jacob very well. Richard may not have understood that he was helping to choose Jacob's replacement, and he may be devoted to maintaining the status quo.
The wild card at the moment is Ilana. Ilana is very likely looking to retrieve Jughead. One possibility, already noted, is that she is working with Eloise Hawking. However, it may not be a matter of controlling the island; instead, based on recent revelations, it may be connected to Hawking's understanding of space/time and her desire to ensure that events unfold in past, present, and future as they must. Ilana's activities might factor into the return of the Oceanic Tribe to 2007.
Alternatively, Ilana's team might be connected to Richard. As it stands right now, beyond Jack and Sayid, he would be the only other person to know Jughead's location at the time of "the incident". Considering that Ben and Locke were gone, and Richard never expected to see either of them again, he could have wanted to take custody of Jughead to bolster his own control over the fate of the island from threats like Widmore.