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Regarding the weakness you point out, that seems to be a direct consequence of assuming that a human being must own the rights to a patent, not an organisation.
But while I know treating corporations as people isn't approved of, this is one place where it does make sense. If a patent is created by a team being payed to do so by their employer, it's not unreasonable that the employer be the owner of the work they produce. You won't achieve your goal of encouraging innovation if the people paying for it are afraid that the work will simply walk out the door once done.