I’m not going to pretend to have a lot of deep thoughts on Evangelion as a whole, but in regards to a lot of the talk about the awkward fanservice this episode, I think the crew hit pretty close to what I’ve always felt was going on there.
Too many paragraphs about fanservice in anime - I'm not good at keeping things short.
Eva deals very heavily in creating an atmosphere of uncertainty and dread through the explicit betrayal of genre expectations. This is seen most clearly in its subversion of typical giant robot anime tropes, as well as broad strokes of characterisation, but I think if you take that same philosophy to all of the scenes in the show I think you can see there was some authorial intent behind the fanservice scenes beyond being there just for the typical reasons.
Fanservice tropes are an (unfortunately) heavily codified feature of a whole lot of anime. The crew pointed out that in episode 5 the show almost inexplicably sets up a cliche’d fanservice trope, but then not only has the characters not address what just happened but follows it with a prolonged selection of scenes where the two involved don’t interact until the traditional punchline of the trope is delivered with Shinji getting slapped - but in a completely different context.
Eva has already used this trick a number of times, starting with Misato’s initial framing in episode 1 being one that would traditionally get a rise out of the male teen protagonist but instead is pointedly ignored by him in a manner that feels like it was written to create tension about the character relationship in those coming into the show expecting the traditional dynamic between them.
Shinji responding to emotionally charged situations in ways that are incongruous with the expectations that other people and the viewers have towards him is a recurring theme in Evangelion, and I don’t think it’s a mistake that he was also placed in a number of sexually provocative scenarios by the writers, to which he defies the manner in which those scenarios are usually resolved in anime.
This is also why scenes that play out exactly as you would expect them to always stick out to me as suspicious in Eva, much like the one between Shinji and Rei at the end of episode 6. After so many emotional scenes subverting expectations, ones like that which play out by the book feel incredibly out of place and, like Austin pointed out, often have sinister undertones.
Do I think this works, though? Honestly, not really. Evangelion has so much ‘incidental’ fanservice that exists in parallel with the stuff written with clear intent to create drama and tension through subversion of genre norms that any point the show could have made through it really ends up diluted and lost awash the sea of shots framing anime butts for no good reason.
TLDR: Ultimately I do think the team were trying to do something narratively interesting with the more prominent fanservice scenes here… I just don’t think they ended up doing it very well in the broader context of the show, and shot themselves in the foot big time by not committing fully to it.
Edit - To clarify, I’m using ‘fanservice’ as a very broad term to refer to any scene involving nudity or a focus on potentially sexualized stuff.