I believe that babies should be called by gender neutral pronouns until they decide they want to be identified as a boy or a girl or remain neutral. I think that in a system like this there would be less stigma around being gay, transgender, or queer. This, in my eyes, would reduce bullying and allow for more acceptance of people of different sexual orientations.
No, babies should not be called gender neutral names, because the majority of children will "Identify" as the correct gender, as in male or female. If no kids knew what their real gender is, then there will be very confused people who have no clue what thwere thing does.
But at the same time you'll have children who don't like their assigned pronouns and as they become aware of this they will be bullied for it as everyone else is called by the gender specific pronouns. Children could all have gender neutral toys and choose their favorite at the age they can choose. I believe that when this happens it would be easier for children to learn what their own minds perceive they shoul be. Children would also have a greater interest in being tought about the roles gender plays in society.