Multi-story buildings are harder to design than one-level projects, it doesn't mean there's inherent problem in them. You just have to follow the books and do the math.

Condensation, airflow and thermal exchange issues are dealt with in any construction engineering curriculum, there are ready solutions to most configurations. If you don't follow them the issue is not with flat roof but with your lack of professionalism: moving condensation to the attic isn't a solution (especially since so many upgrade them to inhabited lofts anyway).