Sarah, I think the most obvious difference for me is the level of fibre they are getting, but if they get it elsewhere then it doesn't matter a huge amount.

My SD was the same when she was younger, to the point where I had to use my teeth in the car to peel an apple because she wouldn't eat it and we had nothing else. She has grown out of it, it just takes patience and just keep asking and they'll tackle the skin when they are ready. I reckon it has something to do with the texture more than anything...
HTH.