The show started in 1999 when 3d wasn't such a popular or viable choice, but 3d is now the thing, so with the movie, they obviously have the bugdtet and can work it into the plot... That is, using it in the above water scenes, far as I understand from the trailer, thus not having to make people watch the "real" sponge et al on a stick like they've done in the series, yet still making the above water world different from the 2d underwater world.
I'd guess those are the reasons. ;)
At least, my guess and put very simply. I'd guess a lot of thought and debate went into how to do it, incorporate 3d or not and how without ruining the show... that is, without going against the look the show has established for over a decade. (Had they made it all 3d, they'd have surely gotten a lot of flack.)