Each season has a clear theme. Season 1 was introductory, 2 was the hatch, 3 was demistifying The Others. As I said, it takes them about 15 eps to tell a seasonwide story. The remaining eps are inevitably filler. This happens with pretty much every show with a plot.
If they plan and produce three seasons and show them in two batches, the middle one would have to be cut in half and interrupted for nine months or so. Narratively, that wouldn't make any sense. If they had done that with season 3, a lot of people wouldn't know where Hurley's van came from. Sawyer's comment to Tom before killing him would have little resonance: he's referencing a small moment we saw more than a year ago, during the first half of the season.
