I often agree about the animated bit, for example I'd much rather see the Alastair Reynolds novels as an animated series. I just don't think any movie can do them justice.
But personally I thought the new Dune movie was really good, I can't wait for the 2nd part.
Macheneries of Empire is another one I feel would only work as anime, not just animated. A lot of things in that, like the description of Kujen's (literal) shadow as like a canvas of fluttering moths' wings (and a lot of other fashion-related descriptions), remind me a lot of Gankutsuou's visual effects.
But personally I thought the new Dune movie was really good, I can't wait for the 2nd part.