Seems pretty obvious to me. After the events of the End of Evangelion, Shinji obviously wanted to escape into a world where he could live a normal life free of all the pain his world inflicted on him. Edd (Double D) is the vessel he chose to become to fulfill this dream. The signs are there. Both Shinji and Double D aren't very confident when dealing with members of the opposite sex and both want to be liked by the other people in their lives. Both only ever make two long lasting friends. Both are noted to be fairly feminine in strength and, sometimes, appearance.
Both also have parents who are rarely there for them. Shinji lost his mom to the Evangelion project and his father, Gendo, simply neglects him. Both of Double D's parents seem to barely come home and leave the poor kid notes as the only means of contact between them. Here is something else to consider, take a look at Double D's hat, [url=http://img4.wikia.nocookie.net/__cb20120130210759/ed_/images/7/72/Edd.1.png]here[/url]. It matches up to the pattern of the Angel named [url=http://img3.wikia.nocookie.net/__cb20130123164807/evangelion/images/1/1e/Lelieldesign.png]Leliel[/url], who coincidentally matched up to the pattern of one of young Shinji's shirts shown in a flashback. Might be a hint at what the Hell is under that hat...
So Evangelion fanboys, how does it feel to know that your series is actually Eddvangelion?
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If I could think of a good means to mix an Ed, Edd 'n' Eddy quote with the Evangelion naming system, I would have posted it instead of this. Hopefully I can (not) think of something later.