I've been to Scotland twice and have played Cruden Bay five times, Murcar once and Royal Aberdeen once.
Murcar and RA are similar in that each have great first nines in the dunes along the sea and the back nines (IMO) are weaker. As an aside, I played both Murcar and RA in 2001 and haven't seen any changes that were made as a result of the Walker Cup. All three are fantastic golf courses and it is tough to have to choose between them.
However, I do enjoy CB the most of the three. It passes the true test (IMO) of a golf course as when I am putting out on 18, I want to race over to #1 and re-tee for another round. The table top green on #2 at CB along with the drivable nature of #3 get the round going. #4 is one of my favorite par 3s in Scotland. The back nine at CB yields lots of fun as well. #13 is a good par 5, #14 with the dugout sunken green and the back to back par 3s are wonderful fun and quirk.
If I had 10 rounds at the three courses, I would split them as:
CB: 5
Murcar: 3
RA: 2