Shinji and Warhammer40K/WMG

When reading this page when I read this:
""Adaptation Distillation - Ignoring, for a moment, its prominent inclusion of another company's intellectual property: if this, and not the first version, had been what was seen in the original Neon Genesis Evangelion, then the history of all subsequent anime might've taken a very different course.""

Neon Genesis Evangelion changed anime and manga forever with its special blend of classic super robot genre (if it really existed?) and the radical and way-out-there ideas that the writers and director came up with. Now, with that historical fact (and ask any anime enthusiast or check any documented study of the subject) in mind, imagine if the original work was as over-the-top as S&WH40K. Imagine what would happen to the history of anime.

My question is how?

Death Note:
 * Light Yagami:the Butt Monkey.

Code Geass:
 * Lelouch vi Britannia:the Butt Monkey.
 * C.C.: Heroic Sociopath.

Haruhi Suzumiya: This would be radically different because Yuki Nagato is a carbon copy of Rei Ayanami.
 * Kyon, not Haruhi, would be the one wishing the world around them was more interesting, while Haruhi would be keeping the entire universe from going to hell on a daily basis, al la Emperor Shinji.

Shinji and Warhammer 40k is one of the alternate universes created during The End of Evangelion
Because if Rebuild of Evangelion could be, why not this?

The future refered to by the Scrolls refers to Shinji and WH40K, not Canon NGE
This theory is mainly based off of Chp 19, part 3, where Gendo realizes that the Trident  fits the prophecy better than the EVAs