The Mystique make up looked really cheap at one point. We don't know what is going on in the scene. She may be trying to mimic the look of an alien race.
Don't let the first movie's plot and version of the Dark Phoenix ruin your perception of this story. The Dark Phoenix story is one of the better X-men stories. Hopefully they go really weird with it. Aliens, Phoenix Force Possession and such. I like what they are hinting at. However, the X-men movies have had a hard time sticking the landing. Besides X-men 1 and 2 and First Class the movies have been lackluster.