It's easy to assume that Kaworu's kindness and affection for Shinji in Q are somehow self-serving or malevolent. After all, Evangelion is kind of a whole series about the multitudinous ways people find to manipulate our protagonist into doing stuff that's bad for him. Almost every major character does this:
- Gendo is obviously the foremost example, starving Shinji of affection and emotional availability, and using shame and guilt tactics to force Shinji back into line out of pure self-serving devotion to his own goals.
- Misato doesn't get off scot-free either -- though her intentions are good, and the pressure she's under is profound, she of all people is most keenly aware of Shinji's emotional insecurity, and she often exploits it by framing piloting an Eva as the mature, adult, or manlike thing to do. It's more obvious in the anime, and particularly in End of Evangelion, but it's an element that's still present in the New Theatrical Edition.
- Asuka can be excused quite a bit for being the same age as Shinji and just as immature, but it goes without saying that her verbal abuse is pretty extreme. In particular, she, like Misato, often frames his anxiety and trauma around piloting an Eva in emasculating terms, though she does it far more overtly. Is this a reflection of her own insecurities? Assuredly. But it's still not cool.
- Mari interacts with Shinji exactly three times ever, but it's probably worth noting that she chose to use one of those three times to question his masculinity for crying after his BFF got super decapitated right in front of him.
Shinji doesn't share a lot of screentime with many other (major) characters in NTE. I don't really have much of a grip on Kaji's role in Shinji's development as a character -- his whole situation is cut a little short in the film version of things. Touji and Kensuke are there, though Shinji doesn't have much of an emotional connection with them. But as far as NERV is concerned, what's there is enough to give you the sense that as in the anime, Shinji is surrounded by people who, while they may care about him, don't hesitate to abuse him for their own ends. This hits a crescendo in Q, when he is emotionally abandoned by what is apparently every single Lilin on Earth. That's, uh, rough.
Anyway, going back to the film series as a whole, there's just two main characters who ever seem to form a truly healthy relationship with Shinji:
There's Rei. Though Rei is sometimes used to coerce Shinji, she really never does it herself. Her relationship with Shinji is on unusually equal footing by Eva standards. They're both immature to similar degrees, though in complementary ways. It's no wonder that, in NTE especially, Rei becomes Shinji's closest friend and primary romantic interest. Though he infantilizes her a bit, they speak to each other in honest and plain terms with little pretense.
Who else does Shinji ever get to talk to without a single layer of pretense?
The answer: Kaworu. Kaworu is a parallel to Rei in a lot of ways. It's a deliberate facet of his visual design, obviously, and he has a similar background to Rei in the lore of Evangelion, but I'm interested here in the thematic parallels. Because while Kaworu is clearly more knowledgeable, more socially savvy, and more talented than Rei (or most characters in Evangelion), I don't think he's actually more mature at all. Kaworu doesn't really "get" Lilin -- that's part of his whole shtick, of course.
It means he fails to really understand the extent or reason behind Shinji's suffering and his trauma around piloting the Evas, and it means he says a lot of callous things to him on their trip to see the outside. But that immaturity is as much of a good thing as a bad one. There's other things Kaworu doesn't seem to "get" -- like dishonesty. See, I think a key thing about Kaworu is that he never actually lies to Shinji about anything, at least not as far as we have any reason to believe. When Shinji asks a question, Kaworu gives an answer, even if it hurts him. And Kaworu freely admits his interest in Shinji, without reservation, in a way that's really unusual for boys -- and that raw tenderness causes Shinji to open up in ways we've never seen. In other words, it's a fairly healthy relationship.
(And yes, I'm definitely one of those people who reads said relationship as romantic on some level -- at least on Shinji's part. If you saw Shinji behave this way around a girl, you wouldn't hesitate to say he has a crush. Weirder things have happened in this franchise than a 14-year-old boy being awkwardly bi, and with far less explicit hinting.)
So when it comes time to sortie Unit-13, and Kaworu encourages Shinji to participate, I don't read that as manipulative. I think Kaworu fully believes he's doing the thing that will make Shinji happy. And I think you need only look as far as this pair of lines to demonstrate that:
(Listening to Shinji talk about why he likes the stars)
KAWORU: Instead of seeking change, you prefer a void, merciless abyss of a world. It's just like you.
(Seeing Shinji's reaction to the devastation of Fourth Impact)
KAWORU: I'm sorry. This wasn't the happiness you desired.
Though we the audience never get to see what Kaworu's proposed version of Fourth Impact would have been, one thing's clear: He truthfully thought he was doing what would make Shinji happy. Though he was sent by Seele, as in the anime, he seems not to have had any intention of actually doing what they wanted -- not if it would hurt the weird boy he's so fascinated by. Instead, he's manipulated. Like Shinji. Like Rei. Like all of the Children. Everything in existence is but a tool for Gendo's purposes.
Obviously, Kaworu isn't perfect. But I don't think falling short of perfection means a viewer should default to assuming malice or devious duplicity on his part. The main thing he's guilty of is hubris, in thinking he could tidily sweep up all of Shinji's problems for him. But evil? That's never been his role.
Kaworu's role in the story is as a moment of pristine clarity -- a true, honest, mutual friend, a look into a world where Shinji isn't surrounded by people searching to use him under false pretenses -- that precedes Shinji's precipitous drop into despair. And in my view, that narrative role doesn't work under the interpretation of Kaworu as some kind of manipulative mastermind. It's so core to Q as a film both in isolation and in the context of the tetralogy so far. If Kaworu is "just another" manipulator, then Q the movie is a series of pretty pictures about a crying boy getting mercilessly ground into dust. If he's a friend, he is the reason for Shinji to keep going. He's the light in the the tunnel that shows Shinji that even at the end of the world, making connections is still possible and still worth it.
Kaworu tells Shinji that the only way to make better music is to try over and over. That he doesn't have to be good at it -- he just has to practice until he's happy. That is a very straightforward message in a franchise that is rarely straightforward about its themes. It's what Shinji will have to do going forward, in the face of despair -- the long and hard trial and error it takes to find happiness on his terms, and not anyone else's.