Most viewers of Neon Genesis Evangelion find it a little confusing and think that there is a deeper meaning to the series and can't quite understand what it is, and many people re-watch it multiple times to try and figure out what the meaning is, with some fans writing long essays or even books trying to determine what the meaning of the show is (along with the meaning of the 2nd movie in its franchise, End of Evangelion, since the first movie Death & Rebirth was just a summary of the series). The reason most viewers find it confusing and look for deeper meaning is they are Pink Boys and SubGenius ideas, cleverly disguised as other things, are utterly baffling to them.
The basic story revolves around the story of X-Day, which is extended from just being one day to taking place over the course of several months in the year 2015 (which the show refers to as the year of Third Impact, Third Impact being a euphemism for X-Day). In the show, aliens known as "Angels" fight humans piloting giant robot-like living monsters known as Evangelions or Evas for short (representing the Yacatisma), with the Angels trying to exterminate humanity, and the humans trying to defeat the Angels. Of course, it is obvious that the Angels are in fact the X-ists. However, in the show, instead of the X-ists (or "Angels" as the show calls them) wiping out all the humans, the humans wipe out all the X-ists, using their Evangelions, which are built out of body parts removed from the first X-ist who came in the year 2000 (the year of Second Impact according to the show, or, in SubGenius terminology, an X-Day drill in which there are some X-ists sighted going by in the sky in a Pleasure Saucer).
Now the show has various factions in it, as well. There is an organization called SEELE which clearly represents the Conspiracy, secretly controlling things from the shadows. There is also an organization called NERV which ostensibly exists to protect humanity from the Angels but is actually secretly controlled by SEELE (The Conspiracy), although only 4 high-ranking members of NERV are aware of this and the vast majority of its personnel are totally unaware that they are working for the Conspiracy (i.e. SEELE) and that the Conspiracy has its own plans to harness the power of aliens allied with them (the Yacatisma, represented by the Evangelions) in order to unify all of humanity into a single, bland, Normal being that lives forever in its immortal body, eliminating everything that makes anyone unique. When all people get unified into a single being, it takes place in a very similar manner to the Rupture, except for the fact that it involves Normals instead of SubGenii and instead of ending up in Pleasure Saucers, they are all combined into a single, ultra-normal being in which they are all the same and all live out that bland normality for all eternity.
NONE of the factions, however, actually represent SubGenii, who, in fact, are not present in Neon Genesis Evangelion at all, although X-ists, the Yacatisma, and the Conspiracy are all there, as well as Normals attempting to fight the Conspiracy and failing miserably. The ultimate theme of the show is that it is impossible to defeat the Conspiracy and that the Conspiracy always wins... since the Conspiracy actually DOES win at the end. At the end of the last episode of the original 26-episode series, all of the characters who formerly had different personalities and couldn't get along with each other now all get along with each other perfectly and all have the same personality, and have all been brainwashed to be exactly the same.
This Normalization of everyone until everyone ends up the same is called the "Human Instrumentality Project" by the show, and it is actually one of the main goals of the REAL Conspiracy in the real world, too, making everyone the same. The show in fact deconstructs and then reconstructs the personalities of all the main characters in order to make them all the same, using Freudian terminology and giving the main character a massive Oedipus complex, in order to make everyone a bunch of identical bland Normals with almost no individual variation at all by the end. Of course, Freudian psychology was found to be completely useless and have no beneficial therapeutic affect whatsoever by most of the prominent psychological and psychiatric associations around the world many decades ago, with people switching to therapies such as cognitive behavioral therapy that actually work, so all of the Freudian psychology in this show is just used in order to help convince people to believe in long-discredited pseudoscience rather than actual legitimate Forbidden Science, one of the main goals of the Conspiracy.
The end of the 2nd movie, End of Evangelion, is a bit different, taking place AFTER the apocalypse and AFTER every single human being was killed and united into a single being, and then that being died, and only 2 people, representing a new Adam and Eve, or perhaps "Bob" and Connie, managed to survive. But NO, they do NOT represent "Bob" and Connie, because in fact they are the 2 most Slackless Normals from the entire show, the characters Shinji Ikari and Asuka Langley Sohryu, both of whom are miserable almost all the time and are about as far away from Slack as a person could possibly be. They have this misery DESPITE being brought back from the dead by the original Adam and Eve, whose names in the show are Kaworu Nagisa and Rei Ayanami, and who try to cheer up these last 2 survivors of humanity, one an utterly slackless 14-year-old boy and the other an utterly slackless 14-year-old girl.
And of course the calendars in the show are all wrong, since as every SubGenius knows the real X-Day and end of the world is July 5, 1998, rather than some date in the year 2015. And the show doesn't have SubGenii or "Bob" or anyone capable of fighting the Conspiracy in it, which is why the Conspiracy is able to win so easily, since it's impossible for Normals to defeat the Conspiracy of Normals no matter how hard they try, as they are part of the Conspiracy themselves and every action they take only advances the Conspiracy's goals.
Of course, that is Neon Genesis Evangelion's main theme. It depicts a world without Slack, without SubGenii, without "Bob" where the Conspiracy runs rampant, and nobody is able to stop it because they are all a bunch of Normals and every action any Normal takes just plays into the Conspiracy's hands (in the show's wording, it is part of SEELE's "scenario"). And the father of the main character Shinji, namely Gendo Ikari, is the leader of the organization NERV that fights the Angels/X-ists and most of whose members think they are fighting for the Conspiracy rather than working for it, while Gendo Ikari reports directly to the Conspiracy (SEELE) and tries to undermine it from the inside, like "Bob". But Gendo is not at all as successful as "Bob", since he is just a mere Normal, not even a SubGenius, and he could never hope to take on the Conspiracy and win. The main theme is, in a world without SubGenii, without Slack, and without "Bob", it is impossible to defeat the Conspiracy no matter how hard you try, and in such a world the X-ists would all lose the vast intergalactic war and the Yacatisma or Y-ists would triumph.
However, the show does not even mention the possibility of a better alternative through SubGenii, Slack, and "Bob", instead just showing us a dark vision of a Slackless world where Normals attempt to fight the CON and fail miserably. So basically the show is pure propaganda by the Conspiracy aimed at convincing Normals to submit to the authority of the Conspiracy because resistance is futile. So along with being the worst kind of conformist propaganda aimed at convincing people to give in to the Conspiracy, Neon Genesis Evangelion tries to cover up the existence of the Church of the SubGenius, "Bob" Dobbs, and Slack, despite the entire show being all about how the events of X-Day would turn out if "Bob" and the SubGenii weren't around.
Then again, there is another possible interpretation that isn't as pessimistic. It could be interpreted that the SubGenii were Ruptured in Conspiracy year 2000 in Neon Genesis Evangelion, successfully, in what the show calls the "Second Impact", and that the events which happen in the show afterwards, almost all in Conspiracy year 2015, the year of "Third Impact", are merely the calamities which befall humans left behind in Hell on Earth after the SubGenii are all Ruptured away, and in this interpretation, the Angels/X-ists that SEEM to get killed are all just faking it as part of a giant practical joke on the survivors of humanity left behind on Earth who mistakenly believe they are winning battles against them. And the reason the Conspiracy is allowed to run rampant on Earth in this post-X-Day, post-apocalyptic wasteland is again, a practical joke by SubGenii and the X-ists against all the Normals. In the end, all the humans except the most slackless 2 of them get wiped out, as the ultimate punchline to the joke, since that slackless pair of 14-year-olds can either repopulate the post-apocalyptic wasteland with their utterly slackless offspring, or allow humanity to go extinct by not having kids. Either way, it is hilarious to the SubGenii and X-ists behind this elaborate practical joke.
Of course, the entire premise of the show and its theme is highly offensive to Discordians, because they believe they can effectively fight the Conspiracy, in fact fight it even better than SubGenii can, without becoming ordained SubGenius ministers. So, along with being a complete ripoff of SubGenius ideas and a cover-up of the existence of SubGenii or of there being any way to fight the Conspiracy, Neon Genesis Evangelion is likewise blatant anti-Discordian propaganda. Of course since the opposite of discord is an accord and thus the opposite of a Discordian is an Accordion, you could call Neon Genesis Evangelion blatant Accordion propaganda. The fact that not a single accordion, meaning that type of musical instrument, appears in the entire series or any of its movies, just makes it all the more insidious... yeti nother coverup, showing how this show is pure Conspiracy conformist propaganda.
Regardless, all of the commercial success of Neon Genesis Evangelion, and all of the countless puzzling over its meaning by the Pinks, shows how profitable the ideas of "Bob" are, and how anybody can use them to become extremely wealthy, even Glorps who make anti-SubGenius TV shows for the Conspiracy. No other anime has achieved the same commercial success because no other anime has so successfully ripped off the ideas of "Bob" and other SubGenii, disguised it as something else, and turned it into a pro-Conspiracy piece of conformist propaganda.
For more information on Neon Genesis Evangelion, albeit FAR less accurate than this rigorously fact-checked article you're looking at now, you can read about it on its own wiki.