It seems in it Peni had a major personality change and appears more somber and depressed now rather than the cute bouncy energetic character from the first movie.
As a mech-user with that sort of negative personality shift, the internet drew parallels with Ikari Shinji from Evangelion, and started swapping her into memorable Evangeleon scenes that Shinji appeared in as a meme.
Her new personality (and outfit) now more closely resemble her original form from the comics.
Her new personality (and outfit) now more closely resemble her original form from the comics.
That and the original comics she's from heavily draws from Evangelion in its aesthetics and its themes of psychological pain, Peni's spiderman/robot pilot outfit looks a lot like a plugsuit and her robot is basically a scaled down Eva in its design.
There's even a cameo of Shinji, Rei, Asuka and Kaworu as Peni's classmates.
