I always find it important to point out the fact that society is technically an impermanent construct, and that context within a moment is just as important as what's occurring in the actual moment.
So in the cases where a protagonist is there as a vessel for the action rather than a character, as with most games where you can choose gender, this option allows for the vessel to fit the player, and thus is important from the perspective that focuses on the player (yes, by this logic, Aiden from Watch Dogs could probably have been a woman as well considering the writing of that game).
Funnily enough, this doesn't mean "I want to play as someone who looks like me" but rather actually creates a nice idea that choosing gender impacts your experience no matter the choice. For example, I've been picking female a lot recently simply because I want the disconnect that comes with that so I can consider my avatar a separate character rather than a vessel. I choose to have the vessel not fit me so I can sit back and go "Now, I know what I want to say here, but what would my Warden do here?" or "I wouldn't have put that gun down in the cutscene, but clearly this person isn't me"
I'll also agree that the gender roles being played out aren't inherently pro or against any gender but rather repetition of tropes that take on meaning through our interpretations, but remaining on subject I'd say that this choice is something that is important less for "adding diversity" but more for impacting player character interpretation, which often isn't thought about due to the fact that they are largely associated as just being an avatar or a static character.
If you are going to offer gender choice, it should be made with the understanding that this choice affects the type of immersion a player feels, and that it is a tool that should fit your game, and this means a bit more than just role-playing.
This is a complex subject that actually brings up a lot of good points about immersion and the interaction between gameplay and narrative that I wish I had a lot longer to hammer out. However, it's a good starting point for a discussion provided we go beyond just looking at it as a measure of equality.