Sometimes people with large birthmarks can be quite attractive! It doesn't seem to have been aproblem for James II. I don't know if it's fair to judge James I of Scotland. He didn't bother to comb his hair or shave for the only portrait we have of him - so who knows?
James and Mary of Gelderland's children: James III was quite runtish, admittedly, but his brothers Albany and Mar were considered very good looking - Mar was so good looking and athletic that James arranged for him to be drowned in his bath.
I agree that MB was the most beautiful Stuart. Mary Queen of Scots was good looking, but possessed also an incredible charm, a sort of inner sparkle! I don't think MB had this sort of charisma but she was physically very beautiful, and had a kind of goodness that augmented her beauty.
Certainly most of the Stuarts were ugly by todays standards. James I, Charles I and William III I would call ugly. Charles II was "ugly handsome". James II was handsomish but, sorry folks, not very exciting. The Duke of Monmouth was very handsome in my opinion!