NGE relied upon this technique -- I'm not sure what the proper name for it would be -- quite extensively, and of course it was brought back for NTE so that the work could reference both itself, NGE, and other works such as Nadia. Here, I figure it would be best to focus on specifically Eva-to-Eva juxtapositions (NTE-NTE or NTE-NGE).
First up is a brief sequence toward the end of Ha where Misato and Eva-01 are weirdly... coordinated, in terms of how these shots are framed, down to the way they move left to right within the frame on each iteration. The fact that Misato's shots are desaturated also disguises this a bit, but the two of them actually share an overall color palette during this scene. Purple, red, orange, black, white, pale blue, and so on. Why exactly is Misato being compared so directly to "Whore of Babylon" Eva-01? I feel like BlueBasilisk could do a much better write-up on the subject than me...
The next one is also Misato-related, and pertains to the changing dynamic in her and Shinji's relationship.
In Jo, they're standing side by side and body language is warm and relaxed. Misato is telling him that he's been a big help, and when she takes her sunglasses off, she establishes more casual terms for their relationship going ahead ("just call me Misato"). Things couldn't be much more different in Q. The two of them are standing far apart, and that distance only grows as the Hirnstamm Tower retracts into the anchoring plug. Misato removes her sunglasses not to open herself up to Shinji, but to unambiguously reveal to him her cold post-3I persona, the captain who has no interest whatsoever in Shinji's "help".
Here's another one, comparing a famous shot from EoE with a big moment in Q. Pretty sneaky. I'm a little iffy on the full implications here.