I don't find Mary an inherently bad-sounding name, but to me, it's faceless, generic, and says nothing. I realize that it's not widely used as a first name at this time, but because it was so overwhelmingly popular for so long, centuries, that is the image it has for me.
I would never ever use it as a first name. The only way I'd use it as a middle name would be if I really wanted to honor someone named Mary. Otherwise, no, because it's filler in the middle name slot.
If I had a daughter named Mary, I'd want to call her by her middle name, since I don't want to call my daughter Mary. But then, I don't know why I'd ever do that, stick Mary first just to call her by her middle name.
I'm of the opinion that Molly should still be used as a nickname for Mary, but I don't like Molly enough to do that.
Well---I've known quite a few Marys, but I'm glad it's not my name.