Yes. I'd love seeing a dedicated perk system for vampires and werewolves. As for how it would be implemented, well, I see it like this ...
Upon transforming into a vampire, for instance, a new skill / perk tree opens up for "Vampire". The level of this skill would represent your level of vampirism, and would increase according to the frequency at which you utilize vampiric skills. For instance, feeding, using Vampire-specific spells such as mesmerizing opponents, masking your vampiric identity so that you can do things in public, and using vampiric charm or fear spells to get things going your way, and... perhaps simply surviving as a vampire. For each night survived as a vampire, you could receive a boost to your vampirism skill, which could decrease over time (perhaps a total of two in-game months to become a full-fledged, level 100 vampire?). This makes sense, as generally, vampires grow in strength the older they are.
I could see a variety of useful perks. One could be feeding on dead bodies to stave off some of the hunger, and perhaps the second level of it could restore some of your health. One could increase your attunement to your vampiric powers and decrease the magicka required to cast them, the next level of it could eliminate the magicka cost altogether, which would be great for those vampires who weren't formerly magic-oriented. Another sensible perk is decreasing the damage done by sunlight, perhaps starting at at 25% decrease, and topping off at a 50% decrease ...because I wouldn't want to see vampires become
too welcome in the sun. And another could allow you to feed on individuals who are awake by mesmerizing them. Yet another could allow you to permanently enthrall someone to your service.
As Tdroid said, your spent perks would be wasted if you cured yourself. So I believe that the vampire skill should level up separately from your character level, and upon increasing in character level, you could receive one perk for your standard skills, and a separate, "Vampire Perk", for your vampiric skill tree.
It's not the most effecient system. Though it's better than the alternative, which could be refunding your perk points. Which might make sense, too... after all, even after being cured, you'll still retain some of the skills you learned as a vampire, and you could redistribute them to your current skills.
But that might be overpowered.
A flawed system, I admit, but after ironing some things out, I think it would be awesome.

Lol, noticed a couple people had similar ideas to me. Good to know I'm not the only one. Might actually have a mod idea in our hands for the future.