AIRPLANES: I tend to glue and then paint because the joint at the wing root seems to always need filler and sanding. ALso, excluding camo, airplanes tend to be one color.
CARS: I always paint then glue. There are so many colors required for cars that it is not possible to glue then paint. For example, I am working on a car that has a red underbody, black frame, steel springs, silver and blue shocks, silver exhaust and silver/gold mufflers. It would be impossible to glue and then paint in that situation.
GLUE: I always scrape paint before gluing. It takes time but it produces a superior joint.