Guys I know who know what they are talking about say that raised-seam metal roof is terrific, Mark. If I were going to build anything, which I am not, ever again, I would use metal. Good looking, too.
My own bias: I have never seen a skylight that didn't eventually cause problems, usually at the worst possible time. If I had my druthers and it could be done, I'd never pierce any roof for any reason. One less thing to go wrong, I figger.
Bob