@ ZOOP, Shinji is the tentative third child. The number on his foot suggests that. Other Shinji-like things couldn't have come out of Unit 01 because they weren't stored in there to begin with. They weren't cloning Shinji, Ripy in Alien Resurrection style. If any active searching was done it would have resulted in finding something or not finding something.
I mean, if they did have the means to return people to humanity, then Rei or Yui might have also been extracted. And if they were, the wouldn't have confused them to the point where they would need a numbering system to catalogue these things. They would be like, "Dude, that's a chick." "Yeah, it's probably not Shinji."
This conversation seems to prove that no one was expecting Shinji to come out:
They weren't expecting Rei to come out. That's why Asuka seems to disinterested in the question being asked, because the correct answer is "Why would she come out?"
Then Asuka cuts to the chase with Shinji:
Right after eluding that no one was expecting Rei to come out of Unit 01, she turns the tables right onto Shinji. Her tone becomes different as she seems to address Shinji specifically with her line. Asuka blatantly tells Shinji that no one in Wille is concerned with one person. Not even him. Why would they be? How would they have known Shinji was in there to extract? Remember, she was in the same state as Shinji was in Unit 01. If Rei was thought not to have existed, then Shinji would also have been thought not to have existed.
It's simple deductive reasoning, really. If A, then B. If no one thinks Rei exists, and Rei was in the same state Shinji as in, then no one thought Shinji existed either.
We remember what happened to everyone else during N3I, right?
Who knows what state Shinji is in? Not Wille, that's for sure. If he's not tanged and unable to return to Humanity then he was either speared to death right afterwards or has become a sacrifice himself. Maybe bot in the same way everyone else has, but in some way. The possibilities are endless, and very few of them would sensibly include "And Shinji was still inside Unit 01 and lived happily ever after."
If no one at Wille, Misato included, is concerned about one person, then why would they spend 14 years, or any amount of time or that matter, planning the retrieval of one person?
Could it be because they think he might be an Impact Trigger? No, it's not that reason. They didn't seem to wise up to that until much later.
But then why put a collar on Shinji if they didn't think he was still an Impact Trigger at the time? It's because the Eva Unit was being unpredictable.
Everything they state as being a reason why they had done what they done comes from two things:
1) Not making a "fuss over one person," which includes making a trip out to space for someone they didn't think either existed or could return to humanity.
2) Weird and unexpected things that occurred only after making contact with Unit 01 in outer space, due to Shinji's unexpected existence.
There's no reason to believe that Misato knew Shinji still existed, what with N3!, Unit 01 getting speared in the back, and it being 14 years of Shinji supposedly dying a slow and painful death from the wounds if he still existed after N3I.
Does it distance Shinji from the others? Yes.
Does this make it difficult for Shinji to be in their world with them? Yes.
Does this alienate Shinji? Yes.
Why, it looks like Anno has placed his audience into Shinji's perspective REALLY well if they're also constantly wondering why everyone's so mean to Shinji if everything seems to be about Shinji, despite the fact that Wille doesn't make a "fuss over one person," and never actually thought he'd return to humanity, as Ritsuko put it at the end of Ha, or even exist anymore, as Misato put it at the beginning of Q.
I mean, if we're gonna judge the actions and thoughts of the characters in this thread, we might as well, actually, you know, judge what the characters are doing and thinking. And both movies support this thought.
EDIT: Actually, watch me negate my own point for a moment. Asuka probably would have believed that Shinji is still alive and well in Unit 01. She calls out to him during battle and stuff, and that's either wishful thinking or something inside her really believes that Shinji's alive. This probably goes back to her experience with an Angel in Ha. Even though they're not the same, they do have enough similarities where it would now be Asuka's turn to vicariously live through Shinji. Final might help us understand more one way or the other.
Miato, on the other hand, probably didn't believe Shinji still existed. After all, if they really went looking in there to extract people, they would have found evidence for not only Rei, but also Yui. Fuyutsuki states that they are both stored inside Unit 01. So if they really are there, going in there and extracting him would have resulted in finding other folks in there too. Misato is either lying to Shinji about the existence of Rei (which would make Shinji's accusation against her a correct one), or she simply doesn't know because they don't have that sort of control over that sort of thing.
I tend to think the latter is most likely. Evidence can always be presented to to contrast that thought, but the movies haven't unveiled it yet. And everyone seems to be reacting like Shinji was an unwanted surprise to them.