First, you should take housing out of the question. Housing will truncate the viewlines and (unless they are large estate lots with only the immediate location of the house disturbed) the lot grading will eleimate any natural outer terrain. For ex., I did a course that fit nicely into the terrain but then along came the housing and destroyed everything outside the course. The 10th was a long 4 that played down a narrow valley that opened to a plain about 50yds from the green. The housing lopped of 40' of the valley sideslopes to flatten the ridges into lots. It doesn't even look like the same course, let alone the same hole.
So, a great course site is one where, by virtue of the terrain, one can fit the course in without the necessity of moving dirt. Most archtects I know deplore having to move dirt and only do it out of necessity. Take Whistling Straits, Great setting, terrible site in that a majority was flat. Dye moved a tremendious amount to create a topography that he felt was needed to make the course what he thought it should be. Unfortunately, the earthworks abrupty end at the property line, which is a bit jarring. Kyle Phillips also moved a bunch at KB but was able to mask the transition better (but if you climb up the slope right of #4(?) tee, you see the sheep grazing on some pretty flat terrain.
I refer to this as "terra-forming" because the terrain is reshape on a macro leel, not a micro, hole only, level. Sure, if one is blessed with a great setting AND great terrain then it can be said it's a great site. It depends, at this point, how the architect handles the great site that will determine the outcome. It is my feeling that the less "taming" of the site that the architect does, the better the final product will be. But it is a fine line. and some find it hard to restrain themselves because they have machinery at their disposal that can modify any terrain drastically in just a matter of hours. When I see a rugged outer area and a tamed course within it, it is to jarring for my tastes. And I find that the opposite is true.