The most liberating and significant event that's happened for us was getting an end date for the show, negotiated with the studio and the network. Before that, Damon and I didn't know if the mythology we'd created was supposed to sustain us over two seasons or six seasons, so it was very hard for us to do any sort of planning.
Plus, in particular with the whole Jack/Kate/Sawyer-in-cages part of the first part of the season:
As for the people in the cages, it's been pointed out to us recently that when we were writing that arc, basically we were trying to negotiate for an ending to the show. We ourselves as storytellers felt like we were trapped in cages. And the story could not progress until it was progressing toward something.
For me, as a LOST fan, I like hearing about these kinds of difficulties with storytelling. Not in the sense of, "A-ha! See! They are making this up as they go along!" Rather, it's just a reminder that this is a TV show -- and not all TV shows last long enough to answer all the questions. LOST was a risk from the pilot episode on -- supposedly it got ABC exec Lloyd Braun fired for greenlighting it since its budget was so high. The show has broken the Twin Peaks curse of making an engaging show now in its fourth season. That says plenty. So, really knowing where the show is going from Point A to M to Z is probably one of the biggest reasons Season 4 has been great so far.
Along those same lines, the Nikki and Paolo plotline is addressed. To me, their introduction (and rather swift exit) seemed to represent the show in a holding pattern. I wondered, "We're hearing about what the extras were doing while the main characters were off in the jungle? Really? Where is this show going?" I never hated Nikki and Paolo, have never met anyone in real life who despised them, and found their flashback episode to be a great way of tying up loose ends with other characters (along with an absolutely wicked final scene). So, I liked how Damon and Carlton stand by where they were coming from, and explaining why the characters didn't seem to connect with the core audience.
Lastly, there's a lot of wisdom in this following quote (which is something I wish I could say more to myself, as well as those fanboys who claim to love something but later want that something murdered when it seems to go in a "wrong" direction):
You have to make mistakes in order to get it right.
Hello! We're all humans here on this planet -- and humans don't make every decision work for everybody. We make mistakes, but we shouldn't feel ashamed when we make them. Humanoids apparently don't mistakes. They don't feel love either. So, what are we really? We're audience members. And I'm looking forward to the rest of this season and the series.