No I would think they would be severely different in how they are used as well (aside from the obvious fact that one of them needs surgery and another is just a pill and that, that is already a huge difference in usage). The reason they need to be controlled and are supplemental to therapy is most probably because they do a major change to the brain. As far as I know they don't have enough research on whatever psychological effects that may occur from forcefully changing somebody from depressed to normal. These chips definitely have the capability of being what you call a "magical happy pill" only problem is that you need surgery for it so you can't really call it a pill.
I think you overestimate how much Emi has changed. Really the ending is a bit too quick so you can't actually judge how much she has changed properly which is a bit annoying
She got angry at Hisao twice. first time was a bit understandable (I do need to read it through again. Mind telling me which scene it was?). Second time was absolutely horrible. When she got angry at her mom I was shocked and angry. She was being horrible towards Hisao and was snapping at him for just trying to be a good partner and trying to help her. Her stubbornness was unbelievable. Oh and about Emi taking responsibility to that I sort of don't see it. It was a more "I'm sorry for pushing you away in general" rather than a "i'm sorry for being so stubborn and hurting you". Heck Hisao had to force that apology out and she just forgot about him for an entire week. And when they meet Emi was just about attack him again for trying to be nice to her
again. Hisao wasn't even white knighting like he was with Hanako (which was really irritating BTW) he was just trying to help somebody he loves just like how she helped him. So yes I am saying that Emi does chew up Hisao.
At the end all I saw was that Emi changed from not accepting help from Hisao about the loss of her father to accepting help about it. Of course that means she is going to stop attacking Hisao every time he tries to help her in that
one specific area. If Hisao tries to tell her that she has a mental issue and needs help from the psychologist imagine how crazy she would go. She hasn't given up on her arrogance and pride. She just let somebody get close to her. The Nurse is pretty close to her and he should at least have recognized her problem and told her about it yet we don't see Emi visiting a therapist like she should be. She may have given up on hiding her problems from Hisao (I don't think she has done that completely anyway. If she was going through a lot of pain she looks like she would just hide it anyway) but how would she deal from getting told that she has problems and needs help? She would go into another one of her fits. She may have changed a lot but she certainly hasn't gotten rid of her stubbornness. She believes that she can do everything by herself. Hisao has helped her a lot and has made her become a better person but there is a limit to how much you can change in a day.
You can't change that much. Emi's stubbornness and arrogance hasn't gone away. All Emi did was accept Hisao as her partner and somebody she can sort of rely on. She still runs away from her problems (both physically and mentally) and is still stubborn and possibly arrogant (she might have gotten over that though).
) change the amount of heat or glucose in parts of your brain or other such similar stuff. These brain chips are much more assertive. 
