I think the key is that the issue generally is that a girl show is generally, well, made to appeal to a niche. Most boys shows... aren't called so. I mean, GI Joe is probably one of the few shows I would say were marketed to boyhood, but that division of boy/girl is more General shows versus the niche/genre that is targeted at girls. I don't tend to consider PPG a girls show since it didn't really focus on appealing to that audience in any discernible fashion other than female leads, but female leads a girls show does not make. MLP is definitely more targeting that demographic and has the clear pieces for it, but it's layered with all the aspects a good show has as well. It's in the girl show genre, but it doesn't believe it can just copy paste the genre and get success.
Sorta like Legend of Korra is definitely not a girls show, despite the female lead, I suppose. Though the whole love triangle thing annoyed the crap out of me because Korra and the older brother had like zero chemistry other than him being the mystery loner.