I agree, great is a qualitative judgement, and I don't claim to have the knowledge to make too many judgments. I tend to look at course that have stood the test of time, and that have hosted a number of major championships. That's why I used Congressional as an example, a great (or close to great) course that was left behind when a PGA Tour event was moved to a nearby TPC course. As a generalization, I'd say that most (maybe all) TPC courses are far from great. And TPC courses seem to make up a large percentage of the course the PGA Tour goes to.
The PGA Tour has to choose courses that are walk-able, accessible, has lots of public facilities nearby, and can fit gallery. There may be a lot of great courses that simply can't host any sort of big event. I'm sure we all think about a course or several where we'd like to see the pros try an event at.