(Since a rebloggable version was requested -
dammit Tumblr why did you have to break Missing E’s reblogging an Ask function?!)
Well, there are three main suspects for being Kaworu’s human genetic donor.
One thing to keep in mind is that Rei Ayanami has Yui Ikari as her human donor and she looks exactly like a mini palette swapped Yui with slightly different front bangs. (And Rei I actually had the bangs “bang on” so to say)
As to Kaworu Nagisa himself…
I. GENDO IKARI
I actually do like the symmetry of Gendo being Kaworu’s base, thus completing the Rei -> Yui -> Mother and Kaworu -> Gendo -> Father symbolism. It also fits nicely with the Oedipal themes that Neon Genesis Evangelion has going on considering Oedipus boinked his mother (love interest, ho!) and killed his father (and we know what happens between Shinji & Kaworu).
Gendo also had the opportunity, being with the Katsuragi Expedition and sabotaging the Contact Experiment , up to the day before Second Impact.
However, the most damning evidence against him being the original that Kaworu is cloned from is how different his character design is from Kaworu. Rei is a mini-Yui, Gendo & Kaworu look completely different, especially with their chins. Even younger student Gendo still has that square jaw back then.
II. DOCTOR KATSURAGI
Another popular suspect for Kaworu’s donor is Misato’s mysterious father, the head of the Katsuragi Expedition. Obviously, being the one in charge, he had ample opportunity to use his own DNA in the Contact Experiment. We don’t have any clear pictures of Doctor Katsuragi (we don’t even know his first name!), but from what we can see, we have a chin facial structure match.
And this is the part where Kaji comes in. As has been shown before, Kaworu does bear somewhat of a resemblance to our resident triple agent. Misato has also mentioned that Kaji reminds her of her father. (She may have been speaking of emotionally instead of physically, but her previous description of her father as someone with a fragile air does not particularly scream out KAJI!).
Physically-wise (as much as we can tell, anyway) Kaworu resembles Doctor Katsuragi the closest of all the suspects. However, if that is the case, Gainax missed a HUGE opportunity with the lack of Misato & Kaworu interactions considering the former’s serious daddy issues. (Not that Kaworu had much time to do anything further in that one episode).
You may have noticed that Kaji, despite any physical similarities, is not listed as one of the top potential donors. That is because back when the Tabris embryo was unwittingly created during the Katsuragi Contact Experiment, Kaji would not have been a triple agent of NERV/SEELE/the Japanese government… he would have been a random 15 year old boy in Japan.
Unlike Misato, Yui, or Ritsuko there is no indication, in either direct NGE canon or supplemental material that Kaji had any familial connections to either the Katsuragi Experiment, SEELE, or what would become GEHIRN/NERV. Sadamoto’s manga even gives Kaji’s background during the catastrophe of the Second Impact which is a survival tale of a young boy in Japan, once again no connection to the Katsuragi Experiment. Kaji is actually one of the least likely characters in Eva to have gotten his DNA down into Antarctica to become Kaworu’s donor.
III. KEEL LORENZ
Numero Uno of SEELE, he certainly seems that he would have the arrogance to order his DNA to be used in the Contact Experiment & its subsequent sabotage. (Gendo would have had to accomplish this as Keel himself was no where near Antarctica at the time).
He is the oldest of the suspects, so some physical dissimilarities are to be expected. His chin is a better match than Gendo’s (not as good as Doctor Katsuragi’s however), but his hairline is quite different. (Although it is possible that Kaworu’s heavy bangs are hiding a crows peak hairline).
Unlike Gendo/Katsuragi/Misato etc, Keel is one of the few characters that did have direct contact with Kaworu during episode 24 and there really was no indication of any sort of connection between them. Not that I’d be expecting anything paternal coming from Keel, even if SEELE did basically raise Kaworu.
Of course, Kaworu’s donor could be the same as Kaji’s killer — basically a random (very pretty) bozo that we never saw onscreen. The DNA used in the Contact Experiment could also have been a mixture of several people’s and thus Kaworu would not be a direct clone of anyone.
It’s kind of strange that there’s no Word of God about this already. I somewhat suspect it’s been discussed in some obscure interview somewhere that hasn’t been translated into English yet.
Anyway, hope that helps!