Great question! I have wondered the same thing.
The text doesn’t give us an explicit answer (what a surprise), but here’s what I think.
We know or can extrapolate a few things about the Nogitsune and how it works:
- If Noshiko Yukimura’s flashback is to be believed, then just two people — a kitsune and a beta werewolf — could defeat the Nogitusune when it was hosted in Rhys. This means it wasn’t that powerful back then. Further, it had been trapped ever since then so it’s unlikely it spontaneously got stronger in the intervening years (if it had, why didn’t it escape?).
- When Noshiko goes to face NogiStiles in the hospital for the first time with her gang of Oni, she seems very confident at first. It’s a surprise to her that NogiStiles is strong enough to kill the Oni without even breaking a sweat. Obviously, something changed between back then and now. What could it be?
To me, it suggests that the difference in Nogi’s power is the difference between the hosts. Nogi was easily defeated in Rhys, therefore Rhys was not a powerful host. Nogi could kill Oni like they weren’t even a challenge when in Stiles, therefore Stiles was a much more powerful host than Rhys.
This fits with other things we’ve seen in canon. We know Lydia’s grandmother expected Lydia to come into her banshee powers at 18, and we know they were kick-started early by Peter’s bite. That means Lydia had those powers already, but they were dormant. It’s likely other people with powers might be the same — for the powers to be present but dormant until they come of age or something kick-starts them.
I think this is the case with Stiles. He’s something — a spark, a druid, a conduit for the Nemeton. Something that hasn’t quite come fully online yet, as far as we know, but something very powerful — enough so that Nogi could defeat the Oni easily by tapping into it.
This is the first part of your answer: the power Nogi used to wreak havoc was not Nogi’s power, but Stiles’ stolen power. I think Stiles is well aware of this, and that’s part of what he was referring to when speaking to Malia.
But there’s more.
Let’s think about metaphors for a minute. Consider a horse and rider. The horse is more physically powerful than the rider, by a large margin, and yet the rider supposedly has control.
But what would happen if the horse decided not to follow the rider’s commands?
The horse follows the rider’s orders for many reasons — training, being bred for obedience, enjoying what they are being asked to do (horses tend to like running, right), and so on. However, if a horse decided to refuse a jump, bolt, kick, or run away, it would certainly be able to, no matter what the rider wanted. The rider’s control is not absolute. It’s more of a give and take.
The horse and rider would be at their best when they both want to achieve the same goal, and the rider is getting the horse to do something it wants to do anyway. If the horse wants to do it anyway, though, who is really in control? This is not a simple question to answer, because horses are trained to want to do things humans want — like pleasure riding or show jumping. Would the horse want to do that if they hadn’t been trained to want it by humans?
Now think of this in relation to Stiles and Nogi. Nogi is not the one powerful enough to kill Oni, that’s Stiles. Nogi is the one with the cunning, skill, trickery, and knowledge to be able to kill the Oni, and to channel Stiles power to do so.
In other words, Nogi is the rider, Stiles is the horse.
It’s bit more complicated than that, obviously.
First, Stiles is not literally a horse, and he ended up being smart enough to outwit Nogi at his own game, and get rid of him. Stiles is both horse and rider now.
Second, even if Nogi got Stiles to do things he already secretly wanted to do — like punish Lydia for not wanting him — that doesn’t mean it’s something Stiles would have done without Nogi’s influence. How much was it Stiles real dark desires and how much was planted by Nogi?
I suspect Nogi was very careful about the things he “rode” Stiles to do. We all have dark sides — jealousy, anger, hurt feelings, and so on, but we have the self-control to not act on them most of the time. What Nogi did, I think, is give Stiles an excuse to act out, or go along with Nogi doing the bad things Stiles secretly kind of wanted to do — like punish people for not paying attention to him. Alternatively, Nogi may have been able to plant those desires in Stiles, so that Stiles wanted to go along with Nogi’s plans.
Either way, I think Stiles definitely felt complicit in Nogi’s acts. Whether he was or not, we can’t know. He might have felt like he was in control, when really Nogi was manipulating him (like Kate did to Derek in order to set the fire). Stiles is still just a young adult, and Nogi is thousands of years old. No matter what responsibility Stiles felt, no matter how much the raw power was his, it’s not clear cut how much control he really had. He certainly seems to have felt like he had some, going by what he’s said, so he at least seems aware that it was his power Nogi was using.
I think that’s what all the chess and go boards were about — Nogi was playing Stiles for his power. Although I think that was mainly a distraction so Stiles’ better self didn’t step in a stop things sooner.
Anyway, that’s how Stiles can be possessed by Nogi, and yet not entirely powerless while possessed by Nogi. It’s how Stiles can feel like he had control. Stiles was the one with the power. Nogi was the one with the skill to manipulate him into using it in particular ways.
I think that’s what Stiles meant by control being over-rated. When you have the power to do anything you want, and an excuse to be able to get away with it (like being possessed by a dark spirit), what’s to stop you? If you’re not a psychopath that must be a pretty terrifying realisation, as well as exciting, and gratifying as well.
It’s no wonder Stiles doesn’t seem to trust himself in S4. Who would with those kinds of questions and concerns running through their head.
Back when S4 was airing, in one of my episode reviews I talked about how I thought Stiles’ Nogi arc was a metaphor for real-world teen violence, and the false sense of empowerment that goes with it. You can find it here: http://cupidsbower.tumblr.com/post/95213090325/tw409-the-puppet-and-the-puppeteer.
Something I think we’ll see next season is Stiles coming to terms with his power, and no longer being afraid to use it.