That would be neat but knowing Bethesda they wouldnt do that.
They will probaly stick with the same formula of just giving rare creatures unique names.
Actually, they have done this. While the enemy may not have been unique, there is a spot in the Grazelands in Morrowind that will sometimes spawn an extra large enemy. IIRC, they were about 3 times bigger than normal. I don't think they were any tougher.
Bethesda loves Easter Eggs and I am sure that some will be peppered through the game. Makes sense as Devs get bored coding in the wee hours of the morning. Creating Easter Eggs gives them something to do while the coffee is brewing.