If treated as a skill, especially as skills are being done in Skyrim you have a fundamental change to your character. Couple this with the new dynamic story and you can have something truly profound. When treated as a skill lycanthropy would obviously grow stronger the more you use it. Perks would allow you customize the power as well, allowing you to choose to stabilize the power or become more destructive. Either way there is a story element about the type of character you choose to play.
I'm imagining myself playing a character and there being some sort of quest or dynamic event that leaves me a werewolf. All of a sudden my character is in a truly desperate position, I'm going crazy, i don't have complete control of my body and I may be being hunted. I can choose to fight to rid myself of the curse, master it, or embrace it. The point being the more you use it, the stronger it becomes, the more - or less - control you have over it. Maybe there is no cure, you just have take the mastery path and suppress it for good. Either way, it is something that has a profound and lasting effect on your character - not merely a spell or greater power.
I'd love to see a system like this implemented but I doubt it, even if lycanthropy is in. It would really compliment my roleplay.