This is near stream-of-consciousness. Forgive me.
People focus too heavily on the masturbation itself when they form a reading of That Scene. There's a great deal going on there and the jerking off is only part of it.
It's important to view everything leading up to the part where he manages to roll her over and her gown pops open. The horror at what he does do her, which amounts to a sort of proxy rape, overshadows the heartbreaking scene that leads up to it. He's literally begging her to wake up, even to insult him.
He wants her back. This is important.
The way they both figure in each other's instrumentality/mindrape/vision quest fugues is critically important in understanding their relationship. Shinji is not in love with Asuka, they have not experienced some grand romance, but the seed is there and that is important. Misato, after all, is alive and awake and Shinji goes to Asuka instead. He expresses concern for her, even though it is selfish.
He does say that Rei III and Misato frighten him, but he's not telling Asuka she's his last resort, he's asking her to come back because he wants something to be normal again.
The second part of the scene begins when he successfully rolls her onto her back and she is exposed. The camera pulls back -and recall that in animation, the position of the camera can be anywhere, and so its positioning is always a deliberate choice by the director, and therefore
means something.
Up until that point, we're on his level, standing next to him, positioned very close to him as he tries to wake her up. When she's exposed, the camera briefly zooms very close to her chest, and Shinji is not in frame. At that point, we're sharing his viewpoint.
It then pulls back. While Shinji completes the act, we're observing from above. Asuka is posed on the bed in a way very reminiscent of a dakimakura pillow, much like this one:
There are others that are even closer but I'm not posting them here and frankly I don't feel like looking them up.
At that point, we are no longer sharing Shinji's viewpoint, but Anno's. We are standing next to him as he takes the role he takes throughout EoE and throughout the series. He's acting as a silent narrator, and the question he's asking here is "are you not entertained? is this not why you are here?"
The essence of that scene, and of the series, is that the director's attempt to consciously insert a theme conflicts with the themes that arise from the work. That is why, in essence, EoE perfectly captures the mind of a depressed person. It goes beyond depicting depression to
become depression.
At this point, Shinji is no longer acting organically, because he is not permitted. He may have naturally jerked it to her but in this specific instance the intentionally visible fictionality of the film is conspiring to make him unsympathetic when what's happening is deeply sympathetic. He is such a broken individual that he can't connect with Asuka on the level he instinctively desires to. Every teenage boy will masturbate and fantasize about girls and women he desires, but Shinji specifically uses the act to separate himself from his emotional urges.
After he completes the act, we switch to a first person view. When he famously comments on his own fucked-up-ness, the camera equates us with Shinji. I am fucked up = You are fucked up.
More to the point of the thread: If you examine all of the times that Shinji is put in a sexual situation or offered sex, his reaction is natural and correct, particularly with Asuka in instrumentality and with Misato.
Misato offering to sleep with him isn't "manning him up", it's disgusting, not just because of their ages, but because of the position of power she has over him and the dependency he has on her. It's not overt, but there is a way to read Misato's interactions with him, all of them, as fulfillment of her desire for revenge by proxy. She's not necessarily calculating about it the way he is, but what she is doing to him is the same as what Gendo does to Naoko and Ritsuko.
Unlike them, though, Shinji knows that it's wrong and resists, even if it's only instinct.
In other words, imagine the same question -why doesn't Shinji sack up and drill these bitches- but switch it out with another character. Why doesn't Rei get her ovaries in order and jump Gendo's bones, or drag Shinji into the locker room and sit on his face? Why did Asuka stop with a kiss and not just tear her shirt off? Imagine if her advance towards Kaji had been met with the reaction she wanted.
See my point?
Eva uses sex as a metaphor for Instrumentality but it does not equate sex with intimacy. In many ways, sex gets in the way of intimacy. Hence Anno's anger over the fabase's reaction and the bitterness that infuses EoE. A point is made with Shinji's relationship with all the girls, but especially Asuka; he ruins what could grow into a strong connection between them by seeing her as a sex object, and Misato does the same thing with him.
There's also the constant theme of Shinji as a girl in a boy's body, not meaning that he is a transsexual but that he highlights cultural expectations for boys and girls- he's not a man and needs to be manned up through sexual abuse by Misato because he takes on a passive role. He suffers and Asuka suffers because they try to force themselves into the role society dictates for them, particularly Asuka; she wants to be the aggressor as much as Shinji wants to passively receiver her affection but their cultural hangups, particularly hers, will not permit it.