I feel there's going to be a backlash against the Aku no Hana complaints by people claiming it's getting hate just because the visuals are different, when that's not true at all. Sure, your average fan will cry about it not being ANIME enough but it's got some genuine issues I don't think you should overlook.
Many people have mentioned this thing about the faces lacking all features if they're far enough (read as: not very far, really) from the camera due to, I'm assuming, the filters on the footage. The funny thing being that if they move towards you, eyes, mouth and nose will gradually appear. Now if this was uncommon I wouldn't mind, but it keeps happening throughout and it's as distracting as you'd imagine.
There's also a recurring issue with rotoscoped pieces, and realistic animation in general, which is the acting being too exaggerated. As an animation fan I obviously don't hate motion, but this case is bad enough to become jarring. It feels like a problem with the base footage, it's kinda over the top and it doesn't feel natural even though the aim of the series appears to be extreme realism. Your mileage may vary greatly here though, I can't deny that it's nice seeing an anime with characters acting for real.
Add more factors like the clash between characters and backgrounds or the apparent lack of an animated opening and you get an overall package that will feel more cheap or atmospheric depending on who judges it. Nagahama's managed to make a creepy manga feel even more eerie, but there's plenty of reasons to question his artistic choices (and things that people will justify as such, when they're just cheap shortcuts).
I wouldn't say Aku no Hana is bad because it's different. It's different, and also bad.