I don't own the Minion Pro font, so that's not an option for me. But I do have Adobe Caslon Pro, which is a serif font I'm fond of.
Is it possible to use the classicthesis.sty and use Caslon Pro instead? I can't see a way currently to do this.
As a second option, I like how Palatino looks from the
mathpazo package, but I prefer the Computer Modern Serif maths typesetting. Is it possible to have the body text in Palatino while having the maths written in Computer Modern Serif?