One other thing you should look at is what kind of film is this? Not just genre, such as science fiction, but is it a surreal film, is it a film with people doing things? Is it a documentary? But you could also go deeper, like, is the story revealed to the audience, or do they know the outcome. For example, you could have a World War Two story presented as a film where you follow the soldier through the city and could be surprised any second, or the story could be presented as an old man telling his grandkids the story. But Genre can also have a great influence in the story. Is your story about a normal man living a crazy lifestyle with all the variables of the situation at a normal stand. Or is this a science fiction where people can twist the elements to do crazy things (example: a car chase where the protagonist flips over the road so the enemy car falls and hits the ceiling.) Make sure to put all these things into consideration, and if you are like me, the story should just fall into place.
But one thing I want to make clear. Don't fall for the overused, "It's just Lego," excuse for a weak story, poor character development, or overall poor interpretation. It's no longer a toy once it's animated. See it as a medium of film. Just because they're little plastic people with printed on faces doesn't mean it has to be a lame comedy or mediocre dynamic duo. You can make a sad film and make people sad. If you're good enough, you could probably make someone cry. If you present your characters well, state a good and interesting story, (That means no Jim and Bob go to school 2) Use your effects in moderation, and create an overall powerful story, the Lego element of the film will melt away and people will actually see characters.