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As much as I dislike the current state of affairs, I can't agree on most of your points. You say balance, but the changes you propose don't seem balanced.
* Working prototype - Is a desirable feature, but not really feasible in a lot of cases. Though I would say, that a patent that is accompanied by a prototype should be granted faster than a patent without one.
* Software patents will not be granted under any possible circumstance - Even though this is tempting, I disagree with that statement in it's entirety. Limit the patent to 2 years, a requirement for the inventor to provide a working copy of the source code, source code for the autonomous module of a bigger software project and let the inventor chose copyright or patent. If the inventor chooses the patent, the source code becomes public domain. A major requirement for the software patent(an actual software patent, not a process patent as they stand today) is that it should only cover the how part. Also, a blind test should be performed on university students, to verify non-obviousness.
* No gene patents. - Not just that, I'd go even further no patents on anything that occurs in nature. Anything that is found to occur in nature is to be deemed a discovery and thus not patentable.
* patent terms should adapt to the industry they belong to - It should be very dependent on the industry and adjusted based periodically.
* Patents must be productised. - That actually clashes with your requirement of a working prototype. However, within 2 years the patent holder has to demonstrate that they either have a product or being used in products or that they have continued to actively develop the product that contains that invention. Remember, that some products have a very long development cycles. Fusion reactors will not come to pass for another 40-ish years.
* Patents should be non-transferable; in other words, they must be tied to the inventor. - Disagree, but sales of patents have to be very restricted.
* Patents will no longer be assumed to be valid by courts. - No. Patents have to be viewed as neutral documents demonstrating that the owner has in fact registered his invention and passed a certain level of scrutiny. Patent text, however, does explain why it is an invention and novel.
* Preliminary injunctions should be a lot harder to obtain. - Preliminary injections should be granted only if irreparable harm is proven. Alternatively if the invention is so essential to the infringing product, that by removing it from the product would stop the product functioning; or a number of inventions constitute more than 51% of the infringing product.
* Instead of merely weighing the costs and benefits for patent holders - One thing to add, if the patent owner has no product(or licensed product) within 6 months on the market only damages can be collected until such a product is released.
* In case of emergency, the state should be able to either temporarily or permanently nullify certain patents. - Already in place.
I will also add a major requirement - the text of the patent has to be a technical text. It should not be a legal text. Any legalese in a patent should result in an immediate dismissal of the patent. The patent text should be very clear to any person in the field and the text has to give enough information to a person of average skill to replicate the invention in it's entirety.
I'll also plug this once more.Software requires it's own IP status, not a system that was designed for writers http://jalexoid.blogspot.ie/2011/07/software-needs-new-ip-protectio...
.ie? The shame... Oh well, from Wiki page of the domain, at least they seem to limit its usage
(though seriously, some less severe restrictions of such kind maybe wouldn't be so bad; less domain hoarding)