Alternate Character Interpretation: Given the nature of the series, it's difficult to assess the motives of the characters, particularly since many of the characters, Ichise and Ran in particular, are given to introversion, and the show's style means that we get little insight into the characters' thought processes except when they interact with each other. For example:
Is the affection from Doc to Ichise mutual or one-sided on her part? Is the relationship akin to lovers, siblings or mother and son? Bit of each, or none of the above? Does Ichise leave Doc on the surface because he never really cared, or because he realized he couldn't get her out of her funk no matter how hard he tried?
Angst Aversion: The main reason why a lot of people don't end up watching this show. It contains brutal violence, no entirely sympathetic characters, pretty much no humor or lighter moments whatsoever, one of the most bleak and cynical views of humanity to ever be portrayed in an anime series, and unabashedly heads towards one of the biggest Shoot the Shaggy Dog endings without ever promising otherwise. It's no wonder that when people read up on it consisting of all of these things, they don't want to put themselves through it.
Cult Classic: The anime is little known on account of being one of the grimmest examples of anime, let alone fiction, ever put to screen, but it has remained a well appreciated series by those who have watched it precisely because it is so dark and unusual, and the unlikelihood of something similar appearing in the near future.
Darkness-Induced Audience Apathy: Due to the series having Black And Black Morality it's kind of about this trope. Nothing the characters do has any hope of saving the world, as it turns out; and there are copious hints that this is the case; but the series is very tight-lipped about it, and up to the moment they turn into plants, it looks like the Shapes (that is, the bad guys) might have lives worth living. And we don't get confirmation of Ran's death until the last few minutes. So the first viewing becomes a sort of staring contest: How much do you care about these characters, and how much hopelessness are they worth to you?
Everyone Is Jesus in Purgatory: Inevitable in a series this abstract. One theory among fandom holds that Kano is telling the truth when he claims that Lux exists only within his mind.
By the end, the series is so heavily saturated in Gnostic symbolism and ideology that you can hardly move for the paranoia, philosophical debate (or maybe "dog fight" would be a better word), and archetypal parallels. The fact that Kano actually thinks he's the demiurge does not help things.
Ho Yay: Toyama is a walking source of Ho Yay in himself, but he seems to have a very particular relationship with Ichise.
And the random member of the Racan who tells Ran he'll "show her a good time" while lustfully caressing her.
Stoic Woobie: Ichise and Ran are both emotionally dead for the most part, but they both receive the cruelest fates in the whole series, with Ran locked into a horrific And I Must Scream scenario until Ichise mercy kills her, and Ichise outliving the rest of the human race before Dying Alone.
True Art Is Angsty: Oh yes. This show is probably one of the best examples of this trope in existence. It has more than earned its title as one of the most dark, depressing and bleak anime series in existence, yet is highly regarded by most of the few people who have actually seen it, despite the fact that even most of its supporters will be quick to admit that it's a tough show to watch and will quickly turn certain people off. It's impossible for it not to fit this category with this combination of traits.
Uncanny Valley: The surface world is pretty much at the dead center of Uncanny Valley.