That being said, there are 900 miles of trails with millions of visitors each year.
Of those millions, most never leave the trailhead. Of the visitors that do venture out on a trail, 90% will stop within two miles of their parking spot. If you avoid Fontana, Cades Cove, Cosby and the AT, you will reduce those numbers even more. The more remote it is, the fewer day trippers you'll encounter.
You'll need a permit, and may need to reserve a place at one of the designated camp sites. While designated camp sites might be a hassle, it is necessary to help reduce the impact of all those people.
That being said, I still prefer the outlying federal lands as it offers more freedom and flexibility for backpacking. I love hiking in the Smokies, but my overnite trips there are maybe 4-5 a year.
I just realized linville gorge is right next door in pisgah national forest. Would it be possible to do linville + cherokee or nanthahala in one 4-5day trip?