On the Tokai Nature Trail each prefecture is in-charge of maintaining their portion of the trail. This means that each prefecture creates maps of their own, and the quality differs by prefecture. The aspect of the trail that I think makes it worthwhile hiking is the uniqueness of the prefectures the trail takes you through. I have been to all the prefectures accept Shiga and Mie before the trail. I lived in Aichi for over a year, and have been to Tokyo many times, but the trail allows you to see a completely different side of the these areas. I think that even if you have been to Japan many times, or you have never been here before the route that the trail takes through these prefectures has something for all. 

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My personal favorite course of the Tokai Nature Trail is Shizuoka prefecture course. Now I have always loved  that area of Japan, so I might be a little bias. The bypass routes allows those who wish to hike the trail to decide how they want to experience the different prefectures. For example if you take the Ena route, you will spend much more time in Gifu than you will Aichi. The Shizuoka routes allows you to take a route either by the coastal region, or though the mountains. While planning your hike I encourage you to look into the different prefectures that the Tokai Nature Trail goes through, and plan your route accordingly.