I think if a story becomes uninteresting because the conflict doesn't come from someones gender then something is wrong with the writing and with the story itself. Sure it can be an element in a story, just like any social separation can be. Class and race are good examples of often used sources of minor or not so minor conflict. But you don't HAVE to have those specific ones. Especially in fantasy. There are plenty of places to draw conflict from that have nothing to do with gender.

Why would it be uninteresting for it to be two women without added conflict from that fact, yet somehow not uninteresting when it's a man and a woman who don't have that particular social issue to begin with?