My favorite points from that link:
"There was a big, mythic architecture which included a lot of what's in the finale, in terms of where we end the show, that we knew way back in the beginning,” Cuse tells SciFiWire in a post-finale interview. "And then, before each season, we'd have a writers' mini-camp and spend a month without any pressure of writing other scripts, figuring out the architecture of the upcoming season. That'd sort of take the artists' rendering and turn it into blueprints, and then, during the season, episode by episode, we built the structure. We allowed ourselves a lot of flexibility to change things around as we were doing construction. It was impossible to have everything planned out, and so it was kind of built in stages."
...And so what? I’m pretty sure pretty much ALL series TV works this way: The creators have some vague idea of how his series will eventually end (Bill reaches Earth, Tony dies suddenly, Jack’s eye closes) and they get together at the beginning of each season and work out as best they can what’ll happen in the next 22 episodes (though they’re probably have more details on the first 11 than the last 11).
Sometimes changes are dictated by what happens with casting. We know Ben was originally going to stick around three episodes and Eko was supposed to stick around till season five. I'd wager that if CBS' "Cane" proved a bigger hit, we'd have seen a lot less of Richard Alpert in the last two seasons.
Who knows what else changed along the way?