Yep. It's funny how so many anime follow this sort of "tropy premise with backstory strip-tease" formula, where they start out in a well-worn theme, but then gradually reveal a dark backstory. Madoka Magica is the absolute pinnacle of the form, each new revelation being as staggering as the last, and yet it never feels opaque and cryptic like Evangelion, and it all makes perfect sense together at the end.
Trigun is another show that does it well. It's a sci-fi western that slowly reveals the origins of the hero and the villain and the philosophical underpinnings of their conflict, as well as the miserable desert planet all the characters live on.
Elfenlied does the same with harem animes, but nobody should ever watch Elfenlied.
Can't forget Utena, the proto-Madoka. It IS as cryptic and opaque as Evangelion, while covering similar ground as (but also completely different ground from) PMMM. It also stands in opposition to Madoka in that it seems almost immune to ongoing commercialization: Rebellion and Magia Record, in its multiple forms, exist, but beyond Adolescence Apocalypse (perhaps in part because of Adolescence Apocalypse), Utena is probably one of the most popular magical girl franchises (very, very few anime have had as much written about it) to never be further capitalized on - and avoids thematic sliding in the process (looking at you, Precure).
The story is about girls who are born with a mutation that causes telekinetic powers and sociopathic impulses, and the shadowy organization trying to contain and control them... and a teenaged orphan boy who has multiple stay at his house, including one prolific serial killer recovering from a massive concussion, as an ultra-dark subversion of the harem anime template.
The premise is ruined by a grotesque amount of lolicon.
Fair enough - I have tendency to ignore lolicon in anime (unfortunatelly it comes with the turf) so I dont remeber it beiing so off-putting.
But I have some vague memory that the violece and gore was quite creative and that there was some intresting contrast created between it and any expectations viewer may have towards normal anime with this kind of premise.
Trigun is another show that does it well. It's a sci-fi western that slowly reveals the origins of the hero and the villain and the philosophical underpinnings of their conflict, as well as the miserable desert planet all the characters live on.
Elfenlied does the same with harem animes, but nobody should ever watch Elfenlied.