The Kaworu appearance suggested to me that you're using the Akira-as-donor angle. But I don't think you provided any description of his physical appearance, so I couldn't be sure. If you have him as Kaworu's dad, though, I'd think that Shinji would be giving him awkwardly long stares, or some such. Another thing to consider, if you haven't, is that Kyoko has "met" Kaworu as well, depending on how you interpret her 'shutting herself away'. Some opportunities here, anyway.

The notion that he's the donor is why I chose the name Akira in the first place -- taken from Akira Ishida, of course, as he would consequentially provide Dr. Katsuragi's voice. Eliminating the donor aspect also eviscerates Akira/Kyoko of one of the very reasons for its inception. Them both having partaken in contact experiments means they're the only two people left on Earth who can begin to understand what the other has been through. This link also cements the Shinji/Asuka parallelism further.

(Preventing him from being tanged or killed as a direct result of the procedure is quite doable, by the way. The details of that CE are almost completely left to the imagination, after all. For Crying Man, I've had the broad strokes of the CE worked out for years now, and getting Akira out of there intact is utterly trivial compared to so much of the migraine that making deep sense of everything 2I entails.)

Your intentions for your own story are, of course, your own, and I have no intention of bending them to my will. For that reason, if you're absolutely averse to what I consider an essential component of "Akira", I'd prefer that you brand your version with a different given name.

August 13, 2024
Kyoko stomped into the living room, fuming with rage. "Damn that Yui Ikari!" she fumed. "Damn her to hell!"
Asuka looked up from her work. "Bad dream?" she asked.
Kyoko's lip twisted up in a sneer. "I wish she was here right now, so I could wring her scrawny little neck!" She closed her eyes, livid, then looked up when she felt a sudden chill in the room. Shinji and Asuka were both staring at her, wide-eyed. She grimaced and said "Sorry. Bad choice of words."
Asuka stared at her for a moment, then shook herself and sighed. "I don't know why you keep getting so worked up about her," she said. "It's not like she could have done things any differently."
Kyoko stared at her, incredulous. "Of course she could have!" she said. "She chose to get in the Eva. She chose to conceal its true nature from the rest of us. She chose to stand idly by while we were killed. And she chose to leave the damn planet!"
Asuka shrugged. "And if she hadn't chosen to do any of those things, we'd all be dead or worse now."
"What are you talking about?" Kyoko asked.
Asuka looked at her. Her mother seemed genuinely confused. Shinji was also staring at her, clearly puzzled.
"I . . . " she began. "We've talked about this. I know we have."
"No," Shinji said. He drew out the word to make the point. "We talked about how she knew about the true nature of the Eva and her choice to keep that information to herself. And we talked about what Professor Fuyutsuki said and her plan to save the Angels. And then a couple of days ago Mrs. Soryu said she thought she wanted to ensure my future, but . . . " He shrugged.
"Well, yeah," Asuka said. The way she said it made it clear she thought this explained everything.
Shinji sighed in exasperation. "Asuka, not all of us are as smart as you are. Throw me a bone here."
"Sorry, sorry," Asuka said, laughing. "I spend so much time dealing with her work that I forget it's not obvious to everyone else."
Kyoko narrowed her eyes. "Explain," she said.
"Well," Asuka began, "take the Eva. If she had told you about its true nature . . . if she had told you the Contact Experiment would kill you, that it would transfer your soul to the Eva, and that I'd have to pilot it, would you have gone through with it?"
Kyoko scoffed at her. "Of course not."
"Right," Asuka said, nodding, "no reasonable person would. So what happens when the Angels show up a decade later and the Evas can't be used to stop them?"
Kyoko frowned. "Tch."
"She still let you and your mother be killed," Shinji said. His expression darkened. "And she still left the Earth."
Asuka sighed. "That was for your benefit," she said softly.
He blinked, surprised. "What? How can you say that?"
"Let's say she intervened in our battle," she said. "Let's say she let you help us destroy the Mass Production Evangelions. What then?"
He fidgeted. "Well . . . "
"Misato and Kaji would be dead," she said, "and so would everyone else who died since Second Impact."
"Even so . . . " he began.
"And more importantly," she went on, "the Evas would still be here."
"So what?" he asked.
She stared at him. "The Evas are weapons, Shinji."
Shinji's breath caught. He closed his eyes as understanding began to set in.
Kyoko looked from one to the other and back again. "What is it?" she asked. "What am I missing?"
"She's right," Shinji said. "No matter their capabilities, the Evas are, and always have been, weapons first and foremost. If they were still around, we'd be forced to pilot."
"That's ridiculous," Kyoko said. "With no Angels to fight there'd be nothing for the Eva to do. No one could make you pilot if you don't want to."
"It's not that simple," Shinji said. "What happens if someone takes Asuka hostage, and tells me he'll kill her if I don't obey? I don't want to fight other people, but if it's to protect her? Or Misato? Or anyone else I care about? Yeah, I'd fight. And so would she. We'd have no choice."
"Hmmm," Kyoko said. She frowned in thought. "So that was her plan? Create the Evas, fight the Angels, and then ensure the Evas' destruction?"
Asuka nodded. "That's the way I understand it, at least."
"But then why didn't she just destroy Unit 01 as well?" Shinji asked. "She had the Lance, didn't she?"
"That wasn't part of the deal," Asuka said.
"Deal? What deal?" Shinji asked. "What are you talking about?"
"Ah," Kyoko said. "Now I get it. You're talking about that nonsense about saving the Angels, aren't you?"
"Yeah," Asuka said.
Shinji shot Kyoko an inquiring look.
"The Lance," Kyoko explained, "is a sentient being. It has its own goals, and while it can be used as a weapon it cannot be commanded. So, if I'm understanding correctly, Yui used the Angels as collateral to convince the Lance, and presumably Lilith, to transform her into a Seed of Life. She would then be able to leave the Earth, and thus ensure you would never have to pilot again."
Asuka nodded. "That's what I think, yeah."
"And I suppose it was just dumb luck that we were killed in the manner we were, and she just shrugged and assumed it would all work out in the end."
Asuka laughed nervously. "Well . . . "
"Hmmm." Kyoko thought for a moment, then shrugged. "She's still a bitch."
Shinji nodded. "Yup."
Asuka sighed, and gave up.

"Shinji?" she asked. They were lying on the bed, side by side, savoring one another's company. She lay with her hands behind her head, he with one arm on his stomach and the other at his side.
"Hmmm?"
"Do you really feel that way?" she went on. "About your mother, I mean. Do you really think she's--"
He shook his head in the dark. "No," he said, "not really."
She was silent a moment. "You synchronized with her," she said. "You had to have known how she felt."
"Yes," he said, nodding. "That was what made is so difficult; I knew she loved me, so I couldn't understand why she'd leave me like that. It didn't make sense to me."
Long seconds ticked by as she mulled things over in her mind. "It must have been difficult for her," she said.
He chuckled.
"What's so funny?" she asked.
"Nothing," he said. "I just think it's funny that you're the one defending her. She hurt you more than any of us."
"Yeah," she said. She frowned. "It was hard at first, studying her work. I couldn't even look at it for weeks. But once I got into it, and started to understand her . . . I dunno. It just became hard to hate her, I guess. And then," she smirked, "mother showed me those pictures--"
"Ugh," he said, wincing. "Don't remind me."
She laughed at him. "What?" she asked. "I thought you were very cute."
"Tch."
"More importantly," she went on, "I saw Yui's face in them. And after that . . . " she shook her head. "There was just no way I could think she was crazy after that. That was a woman who loved her family, not some nutcase with delusions of grandeur. It just didn't make any sense."
"Yeah," he said, distracted. "I guess that's true."
She held out a hand in front of her. "Can you imagine?" she asked. "Actually bargaining with something like the Lance? She must have been terrified."
"You sound like you admire her," he said.
She shrugged. "I don't know about that, but having the guts to do that, and being willing to endure eternity alone for the sake of your family . . . " she shuddered. "I don't think I could do that."
"Oh, I bet you could," he said.
She scoffed at him. "Don't flatter yourself," she said.
He glanced at her sidelong. "I'm flattering you, dummy."
"Oh." She blinked. "Well then," she said, sidling closer to him, "that's fine."
"Heh." He wrapped his arm around her, nuzzling her neck as he did, and they drifted off to sleep.

March 23, 2027
"I didn't even know Mr. Kaji had a brother," Shinji said.
Asuka glanced at him sidelong. She sat with her hands behind her head in the back seat, Shinji beside her as Misato drove. "He doesn't talk about him much," she said. "I never learned why."
Misato looked at her in the rearview mirror. "Heishiro died shortly after Second Impact," she said. "Kaji was responsible."
Shinji's eyes widened. "Responsible? How?"
Misato frowned, deliberating, then shrugged. "I guess it can't hurt to tell you," she said. "Kaji and his brother were part of a gang back then, a bunch of kids scavenging whatever they could to survive. They made a habit of breaking into U.N. storehouses to steal food, and one day Kaji got caught. They gave him a choice: either he told them where his friends were hiding out, or they'd shoot him right then and there. Kaji told them, and they let him go. He tried to beat them back to the hideout, to warn his friends, but he was too late. When he got there they were all dead. He's never forgiven himself for that."
"Jeez," Asuka said, grimacing. "That sucks."
"It was a very different time back then," Misato said.
"Tch. I wonder how his brother will react?" Asuka asked. "I mean, they had to have seen one another in Instrumentality, right?"
Misato shrugged. "I'm not sure," she said. "Kaji seemed to think they'd mostly sorted things out, but he was awfully nervous when he left today. So, I dunno."

Kaji stood before the door of the hospital room, willing himself to enter. He closed his eyes and took a deep breath, then opened the door.
The boy on the bed was as he remembered him: all of twelve years old, wearing a backwards-facing baseball cap and an irreverent demeanor. But the resentment in his face . . . that was new. The boy looked at him, wide-eyed, then scowled and looked away. "Who the fuck are you?" he asked.
Kaji gave him a weak smile. "It's me, Heishiro," he said. "I'm your brother, Ryoji."
"Liar!" Heishiro spat. "My brother is only a few years older than I am, not some . . . some . . . some old man!"
Kaji winced, then pressed on. "A lot has happened since then," he said. "We've . . . the world has . . . "
Heishiro scoffed at him. "You think I'm stupid, old man?" He paused, as tears came to his face. "My brother would never . . . he'd never . . . " He broke off, crying.
Kaji reached out to him. "Heishiro," he began, " I--"
'You sold us out, you bastard!" Heishiro screamed. "You sold us out to save your own skin! You . . . you . . . " he broke off.
"I know," Kaji said. "What I did was unforgivable. There's nothing I can do to apologize, so I won't even try."
Heishiro stared at the ground, fuming with resentment.
Kaji cleared his throat. "Look, apart from that, we have to figure out your living situation," he said.
Heishiro glared at him. "What do you mean?" he asked.
"Well," Kaji said, "we've set you up with a nice foster family. People will be looking after you--"
"What the fuck!" Heishiro exclaimed. "You're just gonna palm me off on some strangers?"
"Well--" Kaji began.
"What the hell is wrong with you?" Heishiro yelled. "You can't just--"
Kaji held out a placating hand. "Hey now," he said, "take it easy. I wasn't trying to get rid of you, I just assumed--"
"Tch," Heishiro spat. "Yeah, I get it. You just assumed. Typical."
Kaji's hand dropped to his side. "What do you want me to say?" he asked.
"I don't want to live with strangers," the boy mumbled.
"Well, after what happened . . . " Kaji trailed off, then shrugged.
Heishiro shook his head. "Forget it," he said. "I'm not doing it." He was silent for a few moments, then looked at Kaji directly. "It's not like I don't understand," he said, his voice low. "They had a gun to your head. What were you supposed to do? And besides," he added, shrugging, "they probably would have caught us all eventually anyway."
Kaji frowned. "If you want . . . " he began. "I mean, you can stay with me, if you like. I guess it'll be kinda weird, but--"
"I don't wanna stay with strangers," Heishiro said. He shook his head. "Fuck that."
Kaji sighed, then nodded. "Okay, then." He laughed. "Man, how am I gonna explain this to Misato? She's gonna kill me."
"Who's Misato?" Heishiro asked.

Heishiro looked around the apartment, then nodded in satisfaction. "Nice digs,", he said. He spied Misato, then added, "Who's the old lady?"
Misato glared at him. "Old lady?" she snarled.
Heishiro nodded. "Yeah," he said, "You're old, and you're a lady. Hence, old lady."
Kaji winced, holding up his hands. "Now now, Misato," he said. "He's just a kid--"
"Tch," she said. "He's a kid who needs to learn some manners!"
Heishiro stuck out his tongue, utterly unrepentant.
Misato grabbed a fistful of the boy's hair, holding his head steady while she stared directly into his eyes. "Listen, you little twerp. I'll cut you some slack since you're Kaji's brother, but get this straight: this is my home. You're here because I allow it, so show me some respect."
Heishiro struggled for a bit, but her grip didn't waver. Neither did her stare. It only took a few seconds for him to give in. "Fine, whatever you want!" he whined. "Just let me go!"
Misato grinned, her demeanor changing in an instant. She ruffled Heishiro's hair and said, "That's better! Welcome to the home of Misato Katsuragi!"
Heishiro groaned as Misato manhandled him.
Kaji smirked. "Get used to it, kid," he said. "Misato's a hardass, but she loves her family. Best to suck it up and soldier on."
Misato grinned. Heishiro whined. Kaji sighed. All was right with the world.