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There are several problems with the OP's suggestions.
First, demanding that a patented item must be "productised", which I assume he means brought to market as a prototype already _is_ a "product", withing a short time frame is simply unreasonable. There are countless reasons why a product may be delayed, countless of which being out of the control of the company producing the item. You do not punish somebody who is already being victimized by circumstances out of their control.
Second, gene patents should be granted so long as the gene sequence is not naturally occurring.
Third, research & development can take tremendous investment, both time & financial. If companies are offered no protection what-so-ever until they've managed to overcome every hurdle in r&d'ing something new, they are far less likely to take the risk in the first place. You can not helping innovation, you are severely hurting it.
Fourth, there is no reason what-so-ever that patents should be non-transferable. Not every inventor or innovator is a business. Not every inventor or innovator is independent. Not every inventor or innovator wants to participate in things beyond the invention or innovating stage.
Fifth, you can't declare all patents invalid unless proven otherwise as it would impose enormous financial burden on both companies and individuals, as well as the court system which is funded by the tax payer. This would be a massive waste of time, money, and resources for everybody. The idea that you, by default, punish everybody all the way down to the tax payer is absolutely ridiculous.
Sixth, assuming judges have the knowledge & experience it takes to make sound decisions as to 'market impact' is absurd. A judge is simply not the proper tool to use to determine how a market will be affected. A single judge should not have the power to deem what's good and what isn't for business. That is not the roll of a judge. A better solution would be a panel or governing body of individuals with the proper expertise making rulings by majority vote.
To sum it up, you make some huge mistakes. You propose rules that hinder invention & innovation by placing restrictions/punishments on those actually doing or paying for the inventing/innovating to take place. You propose placing time limits that are simply unrealistic for real world application. Ignoring the fact that we live in a world based on economics & trade doesn't make it any less true.
Most will agree that the patent system is flawed and easily abused. But you don't solve that problem by going from one extreme to the other, quite possibly making things worse in the end.