Atunyote might have been the most surreal golf experience I've ever had. Immaculate practice area, incredible clubhouse, and quite possibly the nicest entry gate I've ever seen.
Total number of golfers the day I was there? Seven.
It was like a ghost town, and the whole place just had kind of an odd vibe.
Hands down one of the most well manicured courses I've ever seen, but frankly I thought the course itself was pretty boring. I literally can remember one hole off hand right now. And while it was interesting to play for the ghost town experience, I wasn't a fan of the course - and I generally like Fazio designs.
Kaluhyat on the other hand I thought at least had some interest and uniqueness. As John pointed out, there are a few holes where tee transfers are an issue, and it's definitely a course built for a cart. But I found the course to have interesting and enjoyable elevation changes, much better views than Atunyote, and was frankly, just more fun to play. Difficult sure, but no more so than many of the other courses referenced on this site.
Just my two cents, but personally, I'd play Kaluhyat over Atunyote. Didn't play Shenandoah though, so can't speak to that.