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As far as I'm concerned, all the students in Shinji's classroom were candidates to become EVA pilots. That's all I know, but I don't remember if this is ever addressed:

What makes an EVA pilot? I mean, what special quality makes someone more capable of piloting an EVA than others? So basically, all the students in Shinji's classroom had this special quality? What was it?

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Since inline spoiler tags are not possible and I don't want 9,001 spoiler blocks, I'll preface this by saying:

This answer contains many spoilers for the Evangelion series. If you have not watched through at least episode 24, this will contain spoiler material for you.

As a note: Everyone in Shinji's class had lost their mothers (for potential soul salvaging for the Evas), and I believe most had relatives working at or connected with NERV. Each one was also obviously the same age, as a result of being born in the year of Second Impact 14 years prior.

In general, the candidates are chosen by the Marduk Institute, a committee which selects potential pilots for the Evangelion piloting program. They so happen to have listed Tōji Suzuhara at the top of their list, and so he ends up being the test pilot for Unit-03. According to an AU, Kensuke Aida is to be chosen after Tōji, but since there is an incident with Unit-04, this is never seen. There are extenuating circumstances for our main cast, though.

Rei Ayanami was chosen by Gendo because she is, in fact, one of many clones of Yui, Gendo's late wife. This was essentially an executive decision by Gendo so that he could use her for his Instrumentality plans.

Shinji Ikari was chosen, also by Gendo, for a different reason: Evangelion Unit-01 has the soul of Yui Ikari, Shinji's mother, in it, and Yui refuses to let anyone else pilot Unit-01.

Asuka Langley Sohryu was chosen because her mother, Kyoko, was in Germany with Asuka, performing the soul salvaging into Evangelion Unit-02. Obviously Asuka made a good match for a pilot.

And Kaworu, well... Kaworu is just the exception that proves the rule: He was sent by SEELE and is actually an Angel, so he doesn't follow convention. At all.

In the Rebuild continuity, this is slightly different. Rei's reason is the same; Asuka is just a very well trained pilot; Mari has powerful connections; Kaworu works for SEELE again; and Shinji's reason is unknown as of Rebuild 3.0.

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    Also, all pilots were 14 - meaning they were conceived around the time of the Second Impact. – Vixen Populi Sep 23 '13 at 5:30
  • @VixenPopuli Forgot to mention that, thanks. – Killua Sep 23 '13 at 13:10
  • @VixenPopuli: That's interesting. Did that matter though? – Omega Sep 24 '13 at 8:58
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    Is it worth mentioning that Marduk Institute was fake, and as a consequence of such so are the childrens' selection criteria? I forget if it's ever discussed in the show about who makes the real decisions on behalf of the Marduk Institute. – Anatidaus Sep 24 '13 at 22:33
  • @Omega I've always felt that this link between the pilots and the Second Impact was important somehow. But I don't think the series explained why. – Vixen Populi Sep 26 '13 at 5:11

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