Have you forgotten about Stuxnet?
That virus was designed to sabotage industrial equipment that was not connected to internet. It was designed to propagate though removable drives and local networks. And Stuxnet did reach its target and sabotaged it successfully without even causing suspicion.

Imagine that the Chinese/Russians modify Stuxnet (I've read it is quite modular) to infiltrate the UAV control. Imagine that they add module that activates only when the drone enters GPS coordinates of China/Russia. This module could do a number of nasty things. Turning on active radar, so that the drone would shine like a super nova on the radar. Increase the chance of drone crashing. Introduce slight error in missile target coordinates and always hit few hundred feet off the target.

Just the radar thing would be enough disaster. In peaceful time the enemy may decide to ignore it and just track the path of the drone (and hide). In armed conflict, there are missiles that use the radar signal for target homing. It's very likely that a great number of the drones would be destroyed before somebody realizes that the enemy doesn't have miracle super secret drone tracking technology.

The road to hell is paved with good intentions.
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The devil is in the details.

From your description I understand that the new institution would sue "larger companies" on behalf of small patent holders. Now if these small patent holders are patent trolls, this institution service would be like a pipe dream for them. Patent trolls could sue everybody everywhere and expenses would be covered by taxpayers.

I'm not saying that protecting small manufactures is bad thing, but fundamental principles should be established so that this "great power" won't be abused in just one or two decades.

If this institution works like MPEG-LA, then maybe it could do more good than harm.
It's all in the details.

"The nonpatentability of mathematics refers literally to patenting a formula or algorithm without any useful application"
I think the problem here is quite the opposite, the problem is patenting of formula or algorithm for all possible useful applications. And my claim is that if you patent for all possible useful applications, then you haven't actually patented for any of them (because you have not mentioned any).

Take for the example the patent in questions. "The specification makes it clear that 'information storage and retrieval system' refers to a computer system". The problem here is that the computer systems already exist, they existed and they did operate long before this patent was filled and they would continue doing so. The computers do store and retrieve information and they've been doing it for decades in a million of different ways. This patent describes algortitm for working with _abstract_ data. Thus it does not describe any useful application of that abstract data.
How, if the patent said "efficent malloc implementation allowing storage and tertival of heap memory in RAM" or "Efficent garbidge collection in programming language" then these would have been usefual applications, and that patent would not apply for "Efficent file retrival of Flash drives".

So in short, if you patent algorithm for working with abstract data, you patent pure math.

http://www.prisonplanet.com/squalene-the-swine-flu-vaccine%E2%80%99s-dirty-little-secret-exposed.html
It's nice read.
In short, to make vaccine cheaper, they use additative that is very likely the cause of autoimmune diseases know as Gulf War Syndrome.
Vaccines have always been trade-offs, however here we have the following decision: 25% to get GWS if vaccinated or 0.1% of dying from Swine Flu if infected.

Surprisingly enough, but they do. Here http://en.wikipedia.org/wiki/Percy_Schmeiser is the story of a farmer who got his crops contaminated with Monsanto's GMO genes (cross breed from neighbor's crop) and Monsanto went ahead and sued him for patent infringement. And they won.
(Watch documentary "The Future of the Food" for more details)

The biggest problem here is how to revert to non-contaminated crops and how to prevent future contamination (aka stop the wind from blowing).