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 night of the headless horseman. It's got some great voice actors and storytelling but it also has that rubbery shiny early CG that I think a lot of people can't get past.
Oh that's interesting. The movie is on youtube and skimming through it I can get why the artstyle would be off-putting. But it does look interesting and I might check it out. Thanks for bringing it up.