I've said that for a couple of years now, why hasn't someone developed fiberglass hoods and liftgates for all of the 2nd gen on up models. You certainly wouldn't have any paint issues.Also there may be an excellent opportunity for an after market for Hoods and Lift Gates, made from Carbon Fiber or other materials that will hold up over time.
If you get your vehicle repainted find a body shop certified to work on aluminum bodies. They will have the tools and the right paint for doing the job correctly.