While not addressing the situation in the same way, here's my knee-jerk idea for defense against patent trolls:
"If you want to sue a person or an organization, you must pay the legal fees for the defendant, in an amount equal or greater to the amount of money being spent by the plaintiff on legal matters pertaining to the case."
So a small business would get full funding for defense, but it would cost them double to sue someone else. I'd say that's an excellent trade-off. This would dissuade not just patent trolls but any lawsuit where money would be the determining factor for victory.
The Achilles' heel would be enforcement, leading to a new subcategory of legal efforts to ensure compliance. But there's an opportunity for a net reduction in legal action.
There's no need to grant monopoly privileges. Rather, I favor market governed subsidies and grants for innovators to recoup the cost of their effort. The government will play a role in setting up the market and running it. This will be more democratic as people will have a voice to reward inventors for their efforts.
I expect this to be complimentary to innovations that will already arise.
One argument is that patents encourage innovation. The promise of a patent and the rewards to be gained act as a motivating force for ideas. Supposedly.