You can't Deconstruct the Magical Girl genre because there is nothing wrong with it.

You can parody the formula and the tropes, but there is nothing morally wrong with it to truly deconstruct.

Western Comic Book Superheroes abound in Deconstructions because there is something fundamentally wrong with that genre, with it's complex relationship to violence and state power and fictional billionaires, no matter where you fall on the American Political Spectrum there is potentially something for you to find wrong with that genre.  

Individual Magical Girl Warrior shows may sometimes have their own problematic elements, but the core of what the genre is has nothing you can criticize.

Madoka Magica is confused with a deconstruction not just because it's dark.  It's also attempting to be a meta commentary of some kind, referencing earlier works in the genre in ways kind of comparable to what Watchmen does with Superhero Comics, but it's also similar to the way George Lucas was quoting earlier works in Star Wars.  And as I talked about once before this is really the first time one used the term "Magical Girl" in universe.

However the thing about a good Genre Deconstruction like Watchmen is none of it's individual elements were unprecedented in the genre, it's only the way they are put together to draw a different kind of complete picture that makes it unlike anything that came before.  There was in fact no shortage of prior Superhero Comics that had been dark and gritty and/or dealt with similar political themes and social issues.

With Madoka however what makes it so dark in the unique way it's dark (Magical Girl shows had done "dark" stuff before) is tied to what is unprecedented about it.  There is no prior precedent for the monsters the Magical Girls are fighting being all former Magical Girls.  There was also no prior precedent for the wish granting element.  Even before the moment said to be when the show "reveled itself" it had already established a mechanical distinction from prior works of the genre in how the Grief Seed system discourages them from working together as teams.

You might cynically think this all means Madoka was trying to be a Deconstruction but failed because the Genre is Deconstruction proof.  But no I don't think even that has truly happened to this Genre yet.  If Madoka Magica is Deconstructing anything it's the ways one might criticize the genre.

To a certain extent Madoka also plays out like a Greek Tragedy where a tragic fate befalls various characters because they have a tragic flaw.  But none of these tragic character flaws are because of the characters being like a traditional Magical Girl.  I recently watched ClearAndSweet's Youtube videos on Madoka (a series that isn't done yet) and what they've been stressing is how their flaws are all ways in which they fall short of being a traditional Magical Girl.  The title character is the one who is cut out to be a Magical Girl show protagonist but she is being kept from becoming a Magical Girl.

At face value Mami seems like an ideal Magical Girl, her death however is what is commonly misunderstood.  The show definitely at first tricks us into thinking she died because she finally found happiness like what Whedon loved to do on Buffy.  But what the show actually does explicitly say is that her death was the result of refusing Homura's help.  Her stubbornly writing Homura off as an enemy is something a proper Magical Girl Heroine would never do, Usagi is defined in certain seasons by her refusal to write off any fellow Senshi no matter how antagonistic they're currently being.

Each of the four lacks something different.  And the thing is Magical Girls with these kinds of character flaws can be supporting characters in a traditional Magical Girl show, I could probably compare each of them to an Outer Senshi or PreCure Sixth Ranger.  But the key to their ablity to overcome those flaws is the inspiration and example and emotional support that comes from the lead Magical Girl, who for most of this show is being held back.

Another thing that often defines Deconstructions is that they are supposed to be more "realistic" takes on their genres.  Madoka is the exact opposite, and I don't mean by that anything about how it uses it's supernatural elements, I mean how even Madoka's mundane slice of life scenes do not feel like they are happening in the real world.  Sailor Moon mostly takes place in a specific district of Tokyo, you can travel there and visit Rei's shrine or the park where Nephrite died.  So when the Supernatrual stuff happens it feels like it's disrupting a realistic reality.  Mitakihara city however feels like it's made up of elaborate Theater Stages.  Sailor Moon has been adapted into Live Action already and I think it can be again even more faithfully, but Madoka is a story I feel can only work in Animation, how unreal it is is largely the point.

Madoka is definitely not saying Magical Girls would be a bad thing in the real world, it's saying you need to contrive a world much more dystopic then ours for things to go nearly this badly and yet they are still able to set things right in the end.  Madoka is neither a Deconstruction or a Reconstruction, it's a rejection of the very idea of deconstructing this genre. 

Madoka Magica is a show that can work for someone who has no prior experience with The Genre, SFDebris reviews of the show document that perspective well.  But the perception of it's relationship to the genre has (I think mostly in The West) been clouded by how many people watched it who usually wouldn't watch a Magical Girl show, too many people watched it for the darkness not the light at the end of the tunnel.  But in Japan the show was originally marketed without putting the darkness up front, it was marketed to traditional Magical Girl fans, not to edge lords.

Madoka isn't the only show that gets called a Deconstruction of this genre, people also call Utena one.  Utena I do not consider properly part of the genre at all.  It's related, related enough that it's among the earlier shows Madoka is referencing and related enough that any fan of the genre should see it at some point.  I would not ultimately call Utena a Genre Deconstruction at all, what it is working to deconstruct is The Patriarchy, and the values of the Magical Girl Warrior which Ikuhara and Enokido kind of helped build in the first place are one of the weapons they are using to do that.

I don't like to dwell on the negative but I guess I can't close out this post without clarifying that I am anti-Rebellion.