Underrated anime from any genre? Sure.
Flag is an anime version of a found-footage political thriller. It's slow, powerful, and sometimes unsettling. Not for your average fan but it's easily one of the best things in the found-footage genre, period.
Hataraki Man is a lesser-known seinen slice-of-life series dealing with an adult woman with a SERIOUS work ethic working at a weekly magazine. The show goes into the trials and tribulations of adult life while never really sugarcoating it or putting it up on a pedestal. It is a bit over the top and silly at points, but its drama never feels melodramatic.
Kuuchuu Buranko is one of those shows that I still have no fucking clue about. It feels like I never watched it all, but watching it was the equivalent of an animated fever dream. Or acid trip. Maybe a little bit of both. Not quite Cat Soup-level due to the fact that it does all connect and each story in the show makes sense. It's certainly unique, though.
Kemonozume is one of those strange adult titles that manages to be weird and occasionally immature with its overuse of mature ideas. However, it's one of the ugliest things I've ever seen that manages to be even more watchable despite its oddity. It's a straightforward story, too, and probably Masaaki Yuasa's most accessible product.
I will also suggest Shion no Ou despite its major problems because it is a murder mystery based around shogi. It's pretty damn glorious.