My personal favorite for flawed reasons is Madoka because I was there for the live reactions to the infamous episode and it was magical watching everyone lose their shit. It was also my re-introduction to anime after being shamed out of it for liking sailor moon as a kid.
Madoka is great but still i would hold back from the deconstruction label. Dark and fucked up magical stories in the magical girl genre existed before, Madoka just executed greatly while being towards the most fucked up side of things available. Dont think its a deconstruction tho