Having only played Cuscowilla and Tobacco Road I give the nod to Cuscowilla. I will say, however, that I've only played TR once and have played C a couple of dozen times. I definitely want to get back to TR soon b/c it really knocked my socks off in a lot of places.
Also, I would say that numbers 4 through 12 at TR is one of the best nine hole stretches that I've played in a long time.
Cuscowilla is certainly more subtle than TR but then again so is everything. The TR property limits it much more so than C's, especially the wetlands at TR (which were incorporated extremely well IMO). TR is a very difficult walk whereas C flows nicely. I think TR has more mind blowingly good holes than does C, for instance, TR's 9-12th are better than anything at C.
However, TR has some glaring weaknesses that C does not have. For instance, I think the 13th hole at TR is kind of hokie until you reach the green (which is my kind of quirky good) and I found the short par 4s at TR, 5 and 16, not very drivable (especially number 16, just forget about driver there). I happen to be of the opinion that unless a short 4 is drivable it's a waste because forced layups with long irons are no fun.
In addition, I found the vast number of blind shots at TR to be a weakness, especially by the time I got to my approach shot on 15 to a middle pin location that was hidden by the inward pinching greenside bunker. I really enjoy blind shots but I was physically and mentally exhausted by the middle of 15, a bit too much IMO. I also found number 18 at TR a bit of a silly finishing hole. The combination of the blind tee shot and blind second is too much. I'm not sure how much dirt was moved at TR and I'm not sure if the hillock on the left of 18 that obscures the green on your approach was there or was built but it's a bit much for me.
Two final observations re: TR
1) it was the longest playing 6532 yd par 71 I've ever seen and I was hitting the driver great. I shot 38 (three putting 2 and 3 and doubling the 5 par 4th by trying to hit a three iron onto the green from between the trees from the left side of the fairway instead of laying up for a wedge third shot), 44, mostly because my knees buckled on the back nine (I walked carrying my own bag and was wiped out by 15). So even though TR plays mentally tough from the back tees it's not difficult to score there, especially if you're lag putting is on;
and 2) it's practically a desert golf course with a tremendous emphasis on hitting targets, and, IMO forces too many layups and doesn't permit enough swashbuckling heroic plays.