Heh. Okay well, like I said I have some of my own thoughts and, playing a character who changes forms, I've given this a lot of thought. So here goes my thoughts...
Shapeshifting is a non-magical ability. The shapeshifter can turn into anything they've trained themselves to turn in to. However, because there is a very specific amount of body mass to go around, they are limited. For instance, a shapeshifter who is naturally the size of a human MAY be able to turn into something the size of a mouse, but they would have a very difficult time moving, because all of their body mass would be condensed into that little form, making their density insanely high. At the same time, that shapeshifter MAY be able to turn into something the size of a small whale, but they would be almost transparent because their mass would be stretched over a massive area.
Polymorphing, on the other hand, is a magical ability. A polymorpher would not be limited by the restraints of their own body mass. Hence my most common character, Fang, a dragon that dwarfs many others of his own kind, having the ability to turn into a regular size human and still function just fine. However, polymorphers are far more restricted in the forms they can take on. While shapeshifters can take on the basic shape of almost anything they see after only a couple efforts, polymorphers have to be enchanted with the ability to take on a specific form.