This was right when Creator Stephen Hillenberg stepped down from his position of show runner, and handed it over to Paul Tibbit. So with this season under new management, there were some issues that needed to be worked out. After a slew of awful episodes, I think by Season 6, they have finally gotten to show back to speed.
One of the things I noticed about the Post-Movie episodes is how the writers try to come up with more complex storylines. That is not what spongebob has ever been about. If you watch the earlier episodes, Spongebob would take a simple concept like blowing bubbles, and have fun with it for 11 minutes. Now there seems to be a more sitcom format to the show. As much as I have hated episodes such as Karate Island, (whatever the laughing episode was called), Whale of a Birthday, and the Best Day Ever, I have seen some actually really good episodes later on. (Such as The Splinter, and the Slide Whistle one) In these episodes I like how Vincent Waller (of Ren & Stimpy fame) has been brought onto the show as one of the directors, and he has brought a lot more fun animated acting to the show to really help out the show.
I'm sorry I have begun to rample on about the show's current pros and cons, but the point I am making is that once Season 4 started, a new era of Spongebob started, and the show has never been the same. It is a different cartoon now. It is kind of like the Golden Age of Animation when there was many different interpertations of the Looney Tunes characters, with different directors, and everyone has their favorites. Some like the Bob Clampet ones, some prefer Tex Avery. This now applies to Spongebob. Some will prefer the Stephen Hillenberg years, and some will prefer the Paul Tibbit years.