Firstly, I would like to thanks
kuribo-04, who found a spanish site which referenced some details that I don't think were noticed yet, here is the source for those interested : http://www.taringa.net/posts/info/16692739/Detalles-de-Evangelion-3-33-que-no-viste.html
So first, one of the seats in the Anchoring Plug of the AAA Wunder is left vacant during all of the movie, even during the final battle :
A better view of the five entry-plug like structures on the roof of the Wunder, the red stripe really make them look like entry plugs :
Apparently, someone though that a bicycle would be useful in the AAA Wunder!
The logo of WILLE, you can make the letters W, I, L and E from the symbol : one of the two peaks "sectioned" can make a I, and turn the logo by 90° on the right to see the E :
The site tried to make the Tangram-like part of the neo-NERV logo leaf fit, it said that some pieces have been upscaled :
The glyph appearing in EVA-13's entry plug Interface while Shinji and Kawory were breaking the lid form a Tree of Life(saw in NGE in the EVA scrapyard and the giant glowing runes the harpies made in EoE just before starting Instrumentality). Also the 11 runes are actually the same, but turned on different positions
And now, something I finally understood only yesterday, when Shinji was searching for Rei shortly after his arrival in neo-NERV, we see an assembly chain for what the FINAL preview reveal is parts of Gendo's MP-EVAs :
The things on the right are the giant supports used in 1.0 and 2.0 to transport the EVAs through Tokyo-3's rail system(here it must serve to transport the MP-EVAs from their construction site to their storage area or something like that), but I always failed to see what the boxes on the right rail was, and as I said yesterday I finally hit me : those are the big boxes used to transport the EVAs' weapons through the rail system! We see three of them in 2.0 at Mari's feet when she was fighting Zeruel!
[wkimg]File:Eva2-22 C1472 a.jpg[/wkimg]
[wkimg]File:Eva2-22 C1472 b.jpg[/wkimg]