Ultimately, I do not think think the characters would function differently if they were all female. Beckett grapples with the great existential dilemma: the point of existence. Godot, whether he is God, a god, a principle, a philosophy, or strictly human, comes to mean everything to Vladimir and Estragon. The absurdity in their situation derives from the fact that they are unable to ever encounter Godot. They are left with the choice to either commit suicide or continue waiting—to accept that life is inherently meaningless or to create their own meaning.

This is, at least according to the existentialists, the universal condition of all humanity. Therefore changing the gender of the characters would not alter that fact. Women grapple with this struggle just as much as men do. There may need to be some cosmetic changes (name alterations, costume swaps), but I do not think a gender change would affect the essence of Beckett's characters.