@Background Pony #3FF8  
And Pokey Pierce is actually Gendo. (If Doctor Whooves is the Doctor he cannot be Gendo Ikari at the same time, right?)
 
This unicorn: http://static1.wikia.nocookie.net/__cb20120224191005/mlp/images/e/ef/Bloo_ID_S2E18.png is Rei Ayanami.
 
This is Asuka: http://static2.wikia.nocookie.net/__cb20120515034213/mlp/images/c/c0/Firelock_ID_S2E23.png
 
Misato: http://static1.wikia.nocookie.net/__cb20120717020507/mlp/images/4/43/Gray_and_purple_Amethyst_Star_swap_S2E26.png
 
Ritsuko: http://static1.wikia.nocookie.net/__cb20130204074355/mlp/images/b/b3/Serena_ID_S1E3.png
 
Ryoji: http://static4.wikia.nocookie.net/__cb20120311212054/mlp/images/6/6c/Gray_stallion_with_telescope_CM_S2E14.png
 
Kozo: http://static1.wikia.nocookie.net/__cb20130204073548/mlp/images/1/1b/John_Bull_ID_S1E21.png (he also looks like the anime version of the Third Doctor, but we will say that Kozo Fuyutsuki looks like Jon Pertwee less than an apple looks like an orange, and that humans in “Neon Genesis Evangelion” are so heavily stylized they might look completely different in real life, and that their eye colors, hair colors, and facial features can be somewhat metaphorical. “My Little Pony: Friendship Is Magic”, being a completely different series with a different animation style and from different cultures, the stylistic methaporization is completely different in their ponies than in “Neon Genesis Evangelion” humans, meaning that the Pony!Gendo looks more like the Third Doctor than Pony!Kozo does.)
 
Kaworu: http://static2.wikia.nocookie.net/__cb20121231043460/mlp/images/f/f5/Apple_Flora_ID_S3E8.png (Ok, gender does not matter that much.)
 
Keel: http://static2.wikia.nocookie.net/__cb20131212063028/mlp/images/3/39/UES11_ID_S4E04.png (Not going explicitly by color schemes, but he looks evil and strong.)
 
Kensuke: http://static3.wikia.nocookie.net/__cb20120326200126/mlp/images/2/28/Featherweight_ID_S2E23.png (just  
because he looks nerdier than Pipsqueak)
 
Toji: http://static3.wikia.nocookie.net/__cb20120229172615/mlp/images/1/10/Apple_Bytes_ID_S2E17.png
 
Hikari: http://static1.wikia.nocookie.net/__cb20121231043460/mlp/images/c/c4/Pomegranate_ID_S3E8.png (due to looking pepper-y)
 
Maya: http://static2.wikia.nocookie.net/__cb20121231055861/mlp/images/1/1f/Apple_Dumpling_ID_S3E08.png (She is not supposed to look like Shinji, it’s Yoshiyuki Sadamoto s’ fault if Shinji has the same face as all the women in “Evangelion” (or “Nadia”) who are not supposed to be really old, really ugly, fat, clearly an ethnicity not asian or caucasian, based on a real person, or have so-called “Tsurime Eyes”.)
 
Makoto: http://static2.wikia.nocookie.net/__cb20130812221720/mlp/images/9/99/Bill_Neigh_ID_S3E01.png
 
Shigeru: http://static3.wikia.nocookie.net/__cb20120207142145/mlp/images/3/37/UES1_S2E09.png
 
Naoko: http://static1.wikia.nocookie.net/__cb20120224190631/mlp/images/5/5b/UEM5_S02E18.png
 
Kyoko: http://static4.wikia.nocookie.net/__cb20110705211958/mlp/images/2/2f/Ginger_Gold_ID_S1E02.png
 
Dr. Katsuragi: http://static2.wikia.nocookie.net/__cb20120717020508/mlp/images/d/de/Charlie_Coal_ID_S2E26.png
 
Pen Pen: http://static1.wikia.nocookie.net/__cb20120516013941/mlp/images/6/69/Smokestack_ID_S1E21.png (Yup, he’s a pony, not all ponies are humans in the “Evangelion”, and not all humans from the “Evangelion” universe are ponies in the “My Little Pony: Friendship is Magic” universe.)
 
Mari: http://static3.wikia.nocookie.net/__cb20120311212861/mlp/images/3/33/UEM2_S02E14.png
 
Sakura: http://static3.wikia.nocookie.net/__cb20120515034213/mlp/images/5/5b/Key_Lime_ID_S2E23.png (If two people are family related in one universe, they may not be in the other. This is one of these cases.)

@FanOfMostEverything  
Does that mean Dinky Doo is Shinji?

@BigMax  
PFFFT, ahahah! Spelling is awesome! xD

I could get over “Flutter Shy” and “Apple Jack”, but I bursted out laughing at “Twilight Sperkle”.

@Mg127  
I know, we were just joking about it

@platypusmac  
Seclet = secret

@platypusmac  
Seclet 01. She contains the soul of Yui Ikari.

So Derpy’s name in Japan is Seclet?

Oh Japan, you nevel change.