I’ve long been a fan of Bhutan-Trails.org.
I asked editor Rogier Gruys when Bhutan would open to “independent hikers”. Not soon, he says.
As for trekking in Bhutan … you do have to go through a local travel agency. They are not likely to change that …
… you can go with one or two people, and set up exactly the itinerary you want with the agency. The only thing is that you pay US$230/day (for less than 4 people in a group). … But that does include all meals, all local transport, hotel/tent etc. So compared to a typical trip to NY city it is not all that bad!
If I could afford $200 / day I would be booking my next holiday to Bhutan, for sure.
The most famous hikes in Bhutan are the Snowman Trek and Jhomolhari-Laya-Gasa, but Rogier points out there are other great hikes that you can do year round.
Even the hikes out of the capital Thimphu are excellent. In particular, Rogier recommends walking to Tango/Drolay goempas. Or radiotower to Phajoding. “Great views, and a beautiful monastery along the way.”
besthike.com 
I can understand Bhutan’s reluctance for “independent hiking” given how other countries in the region have been trashed by tourists/hikers. Bhutan is amazingly unpolluted, although some trash from trekkers has been left on popular treks. I don’t understand how people can come to a country known for its environmental policies and proceed to leave trash on the trails.
Can you say something about the contents of the Bhutan Trekker’s Guide book you have advertised here? There is no description on its Amazon page.
Rogier Gruys, editor of Bhutan-Trails.org recommends it and knows Bart Jordans.
Rogier tells me Bart’s book has far more information on trekking than does the Lonely Planet travel guidebook.