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.
i think eva genuinely does have some deconstructive elements to it, but they're focused on the high school drama/romcom side of things. part of it is definitely the influence eva would have on those genres and it's hard to say just how much, but shinji's relationships with asuka and rei comes across as kind of a vicious satire on that sort of wish fulfillment high school fantasy that was starting to really take off
anno definitely wouldn't agree that eva deconstructs mecha, the mecha side of things is mostly fairly straightforward, but i bet he'd be willing to agree that it's at least partly a criticism of that sort of otaku brain.