Whether or not there will be a "perk" system is neither here nor there for one simple reason: People's definition of perk vary.
I don't know what Vreg sees as a perk, but in my own opinion, what has been "exampled" above is not necessary. I believe there will already be a "perk" system in the game, and that will be in a form of time-based leveling. For example, in order to increase the damage of a certain flame jutsu, one will need to consistently train and use said jutsu. Vreg also once said that similar jutsu (e.g Fire ball and Fire breath) could possibly have complementary factors. This meaning that by leveling up Fire Breath, Fire Ball will slightly increase along with it due to them being so similar. This would translate over to all aspects of the game, because by time-based leveling, I mean that a player needs to constantly train and use what he wishes to level up, running for stamina and speed, jumping for further height and distance, etc. You get the picture.
Now, like I said previously, the definition of "perk" varies, and I could have completely misread the purpose of this post in terms of what you meant by perks, but along my thoughts, this seems like a perk system mixed into an extensive leveling system. This would result into a game that is not about 100% skill, but as well as time and commitment.
Items are another conversation however. Even though it's pretty dead-set on them being in the game for cosmetic reasons only.
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