Shoreacres was also the first thought I had, but the reason nobody can quite put their finger on what qualifies as "genius" is because everybody has a different definition of what determines a great routing. To me, a golf course with a seamless series of holes and short walks from green to tee on rational ground is the most important quality. As C.B. Macdonald observed: "Mountain climbing is a sport unto itself."
Using this rubric, Succession would have to qualify - regardless of how you feel about the collage of unrelated bunkering and design styles. You putt out and the next tee is never more than 20 paces away. Now, you might have to step over an enormous reptile sunning itself - California pussies like me find alligators a bit unsettling - but the routing feels completely unforced.
There has been quite a bit of mention of Riviera - which I do not think is a particularly clever routing - but Bel Air definitely qualifies. Thomas had to do it with a suspension bridge and a few tunnels, but given the difficulty of what looks like a disjointed site, it is easily walkable and flows together nicely.
There are obviously a variety of reasons that a particular routing is chosen - some aesthetic, but sometimes for practical reasons. When San Mateo coughed up 10 million to redo what is now called Poplar Creek (FKA San Mateo Muni and Coyote Point, AKA "Disgusta National"), I was on the design committee assisting Steve Halsey and Tim Heck. The 1960's slap-dash clubhouse - jammed into a tight corner of the property - was to be torn down and rebuilt pretty much wherever it made sense.
We went through six different routings - the best two wandered the property, but the nines did not return to the clubhouse. The original course did not return either, but the routing was plagued by numerous problems and horrendous drainage issues. Ultimately, we decided (I was vocally in favor of this) to select a routing with two loops of nine holes because it is important to have the option of sending groups off two sets of tees on a public layout. Plus, it encourages more twilight players who do not like finding themselves on a remote corner of the course when the sun sets.
Again, common sense dictated that we settle for a less desirable routing in the name of practicality. Even then, a series of modifications were made after the committee adjourned - including eliminating a terrific bunkerless par-3 as the second hole because of the potential for stack-ups following a short par-5. Instead, in the name of keeping the pace of play flowing, the second was made into a long, difficult, dogleg par-4. In the end, it was a terrible idea because the third hole (par-3) ended up twice as congested. I wish they had listened to me . . . . . .
The considerations and deciding factor for selecting this routing or that routing are often wholly dependent on who is your audience. I'll bet Fazio thinks those discontinuous cart-ball tracks he gouges out of the land are just ducky from a routing standpoint, but to me, walkability is the prime consideration.