The problem is that you only see work in chunks. On the MA I think I remember correctly that we could submit up to 2000 words - that's about eight pages - which is about the length of a short story or a scene or two from a novel. When I'm workshopping in class, the length has to be kept under 800 words. You can get good feedback from that, and I've seen writing improve dramatically as a result, but the one thing you can't get is a sense of the story or novel as a whole.
Seeing a novel in chunks, even a short story in two bites, means that feedback on overall structure and pace is in short supply. Good writing comes to the fore, and editing skills get developed but I wonder if the chunk method may be responsible for the number of writers who get praised for their writing in class and are then disappointed when they send out to agents. I don't know - it's just an idea, and I certainly won't stop workshopping. But if I'm right, then it would pay to get at least one opinion on the piece as a whole before sending out.