I think Nootka is kinda pricey. Based on what I read in Explore mag a few months back, you've got a lot of ferry costs to get to Nootka and then you need to rent a car or hitchhike to the point where you can hire a water taxi to get to the trail. You also need to pay the local natives $40/person to use the trail on top of the BC parks fees and then you need a water taxi back etc. Seems like a great trail, but the JDF is much closer and way cheaper so it depends on your situation. The JDF would definitely be busier though....
There's also the sunshine coast trail which might be nice. I've never hiked it: