It's also worth noting that the NC500 has been if anything a bit too much of a success, apparently there are loads of boy racers doing it and it is equally heavily policed.
That's not to say don't do it, but don't forget that Scotland is absolutely heaving with perfect Morgan roads, such as the B862 (General Wade's Military Road) from Fort Augustus, and the B8004 from Banavie up to the Commando Memorial.
On the Actual NC500 route, personally I would say the only bit where one direction is better than the other is Bealach na Baa and the Applecross Peninsula, which I slightly prefer doing clockwise.