Wow, getting to this super late; I only checked CC on a lark because I happened to see it on my ao3 bio.
There is no denying the first season of the main series had a huge impact on the anime landscape. Its release practically revived the Mahou Shoujo genre. There are series coming out now that are still grappling with the themes of the show—Survivor's guilt. The isolation one feels in civilian life after being a soldier in a combat zone. The beliefs that love will overcome and endure or that, eventually, you can make the right choices.
For most people, it was the first time they were experiencing a subversion of the Mahou Shoujo genre. That said, I feel like the series was the crest of a much bigger wave. I say this knowing that I have a fairly broad definition for what qualifies as part of the "magical girl" genre, so your mileage may vary.
In a 2011 interview, series producer Atsuhiro Iwakami was asked if the popularity of other magical girl shows when they were developing Madoka was part of the studio's inspiration. The interviewer mentions Magical Girl Lyrical Nanoha (Fall '04), and Iwakami-san responds that, yes, Nanoha was an influence. In fact, series director Akiyuki Shinbo was the director of the first season of Nanoha.
Iwakami-san also mentions Pretty Cure (2004-2005) as being another influence—which I can totally see in Madoka and Homura's dynamic. Then again, the sun and moon relationship dynamic—a romance that almost always subtext for a queer relationship—was well established before Pretty Cure. (You know, I bet I could write a pretty solid paper on that).
Anyway, for me, Madoka was a spiritual successor to Elfen Lied (2002-2005) as well as Shikibane Hime (2005-2014) and Gunslinger Girl (2002-2012). Each story dealt with the stress and trauma of being a living weapon, and Madoka is much the same way. Once we, the audience, learn that witches are former magical girls who ended up succumbing to their power and inner demons, there is an undying tension about every skirmish. It was already a given that fighting a witch could lead to an untimely end, but now the very weapons used to defend the world from witches are themselves a threat.
It almost feels like the war with the witches is a somewhat strained metaphor about being a woman trying to live up to society's expectations. A mistake can be fatal in a Witch's Labyrinth. Hesitation? Fatal. Trying too hard? Fatal. Trying to be the hero? Fatal. Failing to understand the Labyrinth? Fatal. Running will only delay the inevitable. A witch's influence will eventually corrupt anyone who came in contact with it. In the end, the only hope for survival is this tiny margin that somehow satisfies all of those competing demands on a magical girl's psyche and body.
In that way, yeah, I feel like it holds up as a piece of anime history.
However, as I am wont to say every time I talk about anime, I would like to see a series on the other side of high school. At this point, I am probably double Madoka's age. It feels a bit off to be drawing enjoyment from the emotional manipulation as well as the mental and physical torture of middle-school girls—except we saw how an adult magical girl show turned out with Magical Girl: Spec Ops (I am still salty about the wasted opportunities in that story).
Perhaps it is the overtly childish character designs that evoke the vague squeamish feeling? Like, consider Madoka nad Homura's designs in contrast to, say, Eva's character designs. Despite Shinji, Asuka, and Rei also being middle-school-aged, I cannot recall ever experiencing the same mildly uncomfortable feeling when watching Evangelion...