For me the first thing that comes to mind is Tales from Earthsea. I don’t think it’s excellent or anything and has plenty of problems but people act like it killed their dog. While it has its problems that have been covered extensively, I think it has a beautiful atmosphere and art.
IMO it would have been better received if it wasn’t advertised as an Earthsea adaptation and was just its own thing.
The live-action “adaptation” of Death Note wasn’t terrible. Calling it an adaptation is a bit generous (more like a separate story in a similar universe) and it nowhere near lives up the source material. But it was alright - seems mostly just hated because of people’s expectations of what it claimed to be an adaptation. In general, media that differs significantly from the source material (even if the source material didn’t exist at the time, like with Fullmetal Alchemist) gets more hate than it deserves.
Black Bullet seems to have some really negative opinions, but I’m a fan of that genre of shows like Tokyo Ghoul where main characters are some sort of social pariah because of non-human features (guess I find them relatable).
Non-animated, but “In Time” 2011 was a movie I enjoyed quite a bit, but found out later that people generally have a slightly negative view of it I think.