To answer the OP's question, yes, my opinion of the show would probably be different if the characters weren't ponies. Nothing to do with the MLP brand, but part of the reason I enjoy watching it is because the non-human characters create a feeling of high fantasy, and help to establish that Equestria is a very different world from Earth.
I also generally tend to find the animation of cartoon animals very admirable - there are details they have to animate that they wouldn't have to with humans, like tails, manes, and a quadruped walking cycle. Not to mention that Faust's art style makes them look so cute, I want to hug them.