The anime is Genshiken (2004), I picked it up on a whim. It's alright so far. Very "by weebs, for weebs". The manga is from 2002.
The 80s and 90s being a pass of the baton from veterans of the early days to more modern staff, which already grew up with anime, and the success of Evangelion and merchandising had some awful long-term consequences even if it was probably unavoidable under capitalism.
The trans depiction in S3 can be a bit sketchy at best in my opinion but it is very much an early 2000s anime, has this vibe that you just can't get these days.
The vibe's one thing, but what's worse about modern shows is that the seasonal format doesn't let the show take any time to develop the story.