the names should be fitting to the role it fills. the warrior type should be something along the lines of Alpha or primal wolf. Stealth could be prowler or stalker wolf. mage would be like arcane or spirit wolf. the name is not as important as the effect it has. say jimmy the mage wants to go primal wolf this would not conflict with his native mage style as the effects are only active wail in werewolf form. with each kill wail in werewolf form would grant you general exp. this can be put into any one of the three branches because it is a separate form and would thus have its own leveling out side of his native form ie human or elf or what ever. his native level will go on as he dose in that native form wail in wolf form you get a standard boot to your base stats so what your native stats are with no enchantments or active effects. so it would add X amount to it. from there depending on what skill branch you go to you can increase your damage or your speed or your ability to summon wolves and or use magic roars. stealth is not going to use higher attack as much as your crit levels will go up. where as if you put your points into primal you get higher damage and defense your only as fast as the base wolf. and the spirit wolf would have base damage speed and defense he would have the magic factor that will give him an edge in combat. and the base of the tree should be transformation time you should get 4 points into this but only require one to move into the other branches. the cap on the wolf should be enough points to max the base and one branch this way if you want to make your jack of all trades wolf you can with out making a god wolf. this keeps it balanced for those who want to specialize and those that like to try it all.
So there would be multiple Werewolf variants? I was preferably hoping to keep it as one, then build the Werewolf as you please with the perk tree. As for magic, if you don't mind me saying, but I believe we should leave Magic to Vampires and other such beings, I believe the Werewolf should be plain physical attacking character. Yet I do like the idea of like increase the effect of roars you had, if that's what you mean.
Maybe upgraded the "Wolf Call"/Summon 2 Wolves will upgrade their duration, damage and overall Health, then perhaps the final upgrade would switch out the baisc spirit wolves for Werewolves or something such as that, and increase the effectiveness of the "FEAR" roar.
As far as names, I don't know if the Werewolves should be named anything different as you suggest Alpha/Primal Wolf for the Warrior like class, Prowler/Stalker Wolf for the stealth and Arcane/Spirit for the mage type Werewolf, I feel we don't need that but again that's just my opinion.
I think however that unlike some Perk trees, alot of skills should be connected similar to a perk "web" so instead of in case of "Heavy Armor" only getting "Fists of Steel" because you want the "Uncondition" skill, I know that's technically tough luck but, if in the Werewolf perk tree some skills moved onto 2 seperate skills 1 being one thing and another being another, say I don't know. For example
Now this example you'd be forced to get the bleeding damage but what if there was an alternative?
"Basic Damage Upgrade 2/5" -----> "Bleeding Damage Upgrade" -------> "Shield Break Upgrade"
-----> "Power Attack 25% less Stamina"------>
The one under it is another of 2 things "Basic DamageUpgrade" leads too which again goes to the "Shield Break Upgrade" so you wouldn't get the "Bleeding Damage Upgrade" if you didn't want it.
But this is just an idea