She is very nicely put together. I really don't see anything glaringly off about her. Nice topline, good bone, pretty shoulder, pastern angles good.
Yeah, she is a little underweight and is lacking some in muscle definition, but it's not horrible. What are you feeding her? (Type of hay, what grain etc). Have her teeth been done recently?
Also, have you looked into using a shoulder guard or light-weight under blanket to help with those rubs?
Her neck isn't bad at all. Just be sure she is working consistently in a correct frame, and that will aid with proper muscling.