For a movie like The LEGO Batman Movie, it could be extremely easy to be dark and dreary.
I mean, it is a Batman movie, and darkness is his thing.
Your mileage may vary though, as some theaters may not calibrate their projectors properly between 2D and 3D showings, which can effect the brightness of any film.
In fact, the color quality of the film is rather impressive, as it’s still very clear to make everything out, and in beautiful detail.