Jim,
I think there is some validity to all of your questions with the exception to the first one about the raters intelligence. I don't think they are all idiots either.
I do think the raters value some different things than the typical GCA poster. Mystique and access are a big thing as evidenced by their consistent ranking of places that are a lot more expensive or more difficult to access.
I don't know that they are biased, but perhaps there are some elements that some other courses might have on the amenities side of the equation that ratings reward.
The qualities of Kingsley from a playability aspect are not lost on people when they only play a place once. The raters I know do notice all of those things like the options off the tee on 14 and hanging out a shot to the right on 16 and letting it roll back down to the green. I only played the course one time and I saw all of that stuff. They know what they are looking at and recognize. It's just that they don't value them as highly as some people on GCA do. They probably think that most people don't really use the slope on 16 unless they hit a bad shot and get lucky, so in their mind it rewards a less skilled player for hitting a bad shot. Also, the points that Andy posted about some of the fall-offs around the greens are valid. Holes 2 and 9 are great holes if you hit a perfect shot from the tee, but if you only hit a marginal shot they can quickly come off as too extreme as you go back and forth over the green multiple times when you think you have hit good shots as I know from personal experience.
Also, I think your last question has some truth to it as well. I think we over glamorize some courses on here. Kingsley is probably the poster child for this. I personally enjoyed the course a great deal and was very thankful to play with Mike DeVries and Brad Klein on my one visit, but there were several parts of the course that I thought were not as great as others. The stretch of 10 through 12 I think is a good stretch of holes but it is not world-class for lack of a better term. I think the width of the fairways on some holes is almost too wide. The options on several of the holes, like 1 and 14, are not something that benefit a person that doesn't hit the ball a long way off of the tee. Then you throw in the controversial nature of holes like 2 and 9. There are a lot of things there that can seperate a very good course from being a great course in the eyes of a rater.
Basically, I think Kingsley does a lot of things very well. There are some wonderful holes throughout the course that are even world-class in my mind. Holes like 13, 15, 16 and 17 make for a wonderful stretch run in my mind. The front nine has one of the most unique par threes I've seen on the 5th. I love the 3rd green, probably the scene of my best putt ever that didn't go in. But in the end, I can see why it doesn't make the top 100. In comparison a course like Crooked Stick that is #100 in the latest rankings of one of the magazines is a course that I consider comparable to Kingsley in total quality. But would I say it is better, perhaps, but I could easily see how someone could not. But then if I compare it to a course that I think is top 100 quality like Old Town, and superior to Kingsley and Crooked Stick by quite a distance in my mind, but it isn't in the top 100. So it doesn't break my heart when Kingsley doesn't make the top 100.