It's not that the clothing was added, it's that it's very stereotypical for girls to only wear skirts, especially in a school that doesn't have a set uniform and has a wide variety of female characters. Plus, if you look at promotional material for Equestria girls, the material shows some of the cast very VERY out of character. For a show that was meant to encourage girls to be anything they wanted, they didn't really set the bar that high.
In my opinion, it's a bad spinoff. They COULD'VE done well with it, but they decided to stick to a merchandise mindset and in my opinion, it was the wrong way to go.
My opinion.