Do not sacrifice the story for the gimmick. If your script is all about delivering 3D thrills and does not focus on a compelling story or interesting characters, the audience will be easily alienated and fail to follow your story. Your 3D script needs to be strong. Develop characters with strengths and flaws. Create conflict among characters. Make your characters believable and human so they will fail at times.
Focus on a worthwhile subject and allow that to be the crux of your script. Your script needs to have a solid foundation and from that the 3D ideas can blossom and grow. A film like "Avatar" had stunning 3D visuals but was anchored by a story containing archetypal heroes and villains, high stakes, lush settings and identifiable story elements re-worked to use cutting- edge technology. For your 3D script, look to "Avatar" as a template. Part of "Avatar's" success was that it had a strong social commentary about environmental issues but was not didactic or preachy in its execution. All scripts do not need to have an underlying meaning, but it certainly helps.
Write a script with a specific genre in mind. The best 3D scripts lend themselves to a particular genre. You don't see any romantic comedies or courtroom dramas done in 3D for a reason. Science fiction, superhero, animated and action-oriented films embrace 3D. All film genres have certain expectations, models, clichés and conventions that can easily lend themselves to 3D. Study the genres you want to write about and you will see other possibilities for the 3D experience.
Write like there are no limitations and your expectations can be better satisfied. Don't allow your first few drafts to be hampered by the enormity of a 3D budget. The 3D technology currently being used is expensive and costs more than 2D films, but don't let these factors affect your script. Don't sidestep the big 3D climax where the aliens blow up the moon just because you fear the logistics of actually filming such a sequence. Subsequent re-writes and revisions can even out such particulars. What is important is that your early drafts be clear in their conception and vision. It's always easier to remove large portions of action and special effects than to lack any spectacle to start out.
Study your craft. Write a good story and convey a powerful script. Read about screenwriting. Review the screenplays for your favorite movies. Watch movies with similar themes to yours and go see some 3D films. You must do some research and development if you really want to write something distinctive and specific.