JP,
By flow I mean the relationship of the individual holes to each other, primarily in close sequence. For me a course is superior where the holes have different looks and require a variety of shots.
Depending on whether the wind is blowing down canyon (from the N, NE as it was when we were at RC this spring) or up, RC has two or three stretches of holes which can play very similarly. I suspect that day-in and day-out, the wind at RC is a much bigger factor than at Cusco. With firmer ground and long stretches of holes going in the same direction, raw yardages and par don't really mean all that much there. I suspect that this is part of RC's charm.
The front side in particular seemed to play very short. And even if you take into consideration that the short par 4 (#7 or so) was being played as a par 3 because of the flood damage, it is still normally played with a middle iron of the tee followed by a short iron to the green.
I thought that the two short fours (south orientation) and the two fives going north (9 & 10?) are overly repetitive, though very good holes in their own right. On a particularly windy site, it would have been better to orient these similar holes in opposite directions (though I understand that perhaps the land or the green sites didn't lend themselves to what might be considered a formulaic idea).
For the most part, Cusco has the golfer reaching for all types of clubs throughout the round. The one exception that I see is the very demanding, long par three #8 with a reverse-redan type green, followed by the very difficult par 4 #9. Here, I think that a back tee adding another 50 - 100 yards would provide more interest and balance to the course, but apparently Coore doesn't like to follow a hard par three with what he would consider to be an easy par five. Personally, I think that the way it is, the powerful hitter has a huge advantage on both holes, whereas adding some yardage would make the 4 more elusive to that guy without doing the same for the shorter player to get his 5.
In any regards, both Cusco and RC are very high on my list. Perhaps I just like the pines, lakes, and greener, rolling terrain of GA a bit better. Both courses do an excellent job of exposing one's weaknesses, particularly with the short game. Cusco #5 clearly showed the schizophrenic nature of my game as I made 6 from a perfect lie 40 yards from the pin the first day, and 2 on Sunday when I chipped in from 40' or so.