A lot of anime deal with identity, but in different ways: whether it is the all-encompassing, driving force behind the movie and series extravaganzas that are Ghost in the Shell and Evangelion or as an undercurrent to more prevalent themes like with Guts in Berserk or Faye in Cowboy Bebop, it is fair to say that many different anime use identity as at least part of their narrative thrust. Even looking at disparate, popular shows like Bleach and Naruto reveals a simplistic version of the theme with the push to become strong and protect - a topic that is an essay in itself. It's only when investigating beyond the obvious that it becomes apparent identity is prevalent in so many different genres of anime that it begins to reflect how they were conceived and upon the creators themselves.
how flippantly cyborgs view gender when the possibility of reproduction is removed
Identity is a wide and multitudinous topic that has been researched by psychologists and philosophers alike for centuries so it's no surprise it is present in a culturally reflective medium as anime. Perhaps the most subversive and comedic is gender identity and the question of what defines gender. The earliest anime I can recall that toyed with this is Ranma ½ which had the titular protagonist switch from one gender to the other with the application of cold and hot water - it is played for laughs more than as a thoughtful treatment on the subject but the enforced gender switching is in so many other series from Kashimashi to Kämpfer that it can hardly be ignored. This is without mentioning the less extreme sex swapping with cross-dressing which has of course birthed one of the most cherished anime cultural staples: the trap.
Rewatching Code Geass R2 set my mind working on something that has been gnawing at me for a while, and it's only recently that the semblance of an answer began to take form. The part in question takes place towards the end of the season and is when the Emperor's plan is revealed to Lelouch concerning the Mental Elevator, C's world and the Sword of Akasha: that of unifying the world into a single, super consciousness. Depending upon the anime one has watched this will likely be a familiar concept and one that has underpinned many influential and subversive series.
everybody ends up all warm and fuzzy and with a greater understanding of Mayan philosophy
The most obvious proponent of this concept is of course Evangelion which constructed elaborate systems based upon Jungian psychology, theology and science and implying that the next evolution of humanity isn't as discrete individuals but as an amalgam. Without delving too deeply into the labyrinthine plot of the series and movies, End of Evangelion demonstrates this with everyone melting into a fluid, whereas the final episodes of the series give a fractured glimpse at the emotional montage Shinji suffers during this. Released in 1995-96, this was mostly the result of Hideaki Anno who it is anecdotally said spiralled into neuroses around the half-way point of the series which is coincidentally when it shed all pretences of being a fluffy children's show and went full bore for dark and symbolic.
