Found this post looking to see if there was anything useful on Bhutan on Flyer Talk.
I can see you got no replies.
Unfortunately I can't be much help either.

But it's interesting to note that you now only need to pay $100 USD\day development fee instead of $200 as previously.

I think your problem may be you not seeing it from the Bhutanese point of view.
The guides and the organisations around tourist are providing a lot of income and they don't really want you to wander around on your own for that reason as much as anything else.
Travelling indipendantly is going to be more expensive than organising something as part of a group. Since one guide can 'guide' 22 people.