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>the biggest problem has been granting patents for inventions that at least in retrospect seem non-novel or obvious.

I don't agree that that's the biggest problem. I think the biggest problem is that patents are abused to stifle competition by refusing licenses or putting untenable fees on them. No one would have cared about Nintendo's D-pad patent if they'd just put a reasonable license fee on it. On the other hand, a patent like MP3 I would argue is quite legitimate, but putting a patent on a coded just makes interoperability more difficult. If MPEG had charged licenses for decoding chips and explicitly allowed software implementations, that would have things so much more smoother.

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It would be better to allow codec patents only on the encoder. Once you have encoded data, there is only one valid way to decode it so everyone should be able to implement that. That is, the general decoding mechanism at least - you could still have novel implementation details.
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That's one problem. 25 years is also a really long time in fast moving fields like software, microchips, etc. And the format the invention is "published" as is essentially a legal document, often largely written by lawyers for a target audience of patent clerks and other lawyers, not a technical specification written for engineers and scientists. And the is an incentive to omit or obscure details important to actually replicating the invention.
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