If they could have had children.
Leonardo would have wanted boys not because he doesn't like girls but because boys have an easier way through life. Especially if they had a non-traditional start. A bastard boy may still find an apprenticeship and make his way up in the world just as Leonardo did. So why wouldn't the same be true for a boy with two fathers?
Ezio he wants girls. He doesn't quite know why. Perhaps it's how close he was growing up with his little sister or perhaps the knowledge that people consistently underestimate girls and so they're more likely to survive like his mother and sister did when his father and brothers died. But I think it's cuz he's always rooting for the underdog in any situation and he knows that girls are deeply underestimated
