I think if they want to make hunting a valuable activity in Skyrim, they should implement the "chance" system where you always have a chance to come across valuable preys or body parts from a certain prey or plant.
When I played STALKER game, before they decide to take out the mutant body parts, I was actively looking for mutants and killed them for their body parts, that's because not every mutant has collectible body parts, and they worth a lot of money once you find one. I think this should inspire the hunting system in Skyrim.
In Oblivion, you find valuable body parts very often in animals and they worth very little money, and all body parts worth the same without difference in grade.