Patrick,
Like you, I am fascinated by how someone looks at a piece of land and "sees" a golf course. As I am wholly lacking in artistic ability, I am very, very hesitant to criticize routing, because I can't offer alternatives. I appreciate what I see, but can't see more, if only because I don't know where property boundaries, wetlands, etc., might be.
However, I do think that GCA's may have "unfortunate" routings imposed upon them by various constraints such as real estate or environmental concerns. One example would be a course that is fundamentally unwalkable on a piece of ground that should be emminently walkable because of long distances between greens and tees. That IS bad routing, but not due to the architect, I would assume. There are, of course, a zillion such courses in real estate developments. Many are wonderful layouts in every other respect. I don't know if that qualifies as bad routing or not.
My home course was built in two stages, and on the "new" nine, environmental constraints altered the green location of a par five, changed a par four into a par three running in the same direction as the previous hole (LONG walk back to the tee), and prevented a cool double green to be shared between a par four and a par three that would have made both holes much longer and more interesting. The yardage of the course was shortened by about 250 yds., par reduced from 71 to 70, walk times slightly increased, and one too many short par fours ended up on the course. I'm sure to some that don't know all of that background, it appears to be "bad routing"; actually, the GCA did a great job of shoehorning in holes that retained shot values given the limitations imposed on him.