Exclusive rights versus remuneration
The problem with creating a new industry like aviation and electric cars is exclusive rights, not that the patent holders get paid. A key quote early in the Planet Money podcast is at ~4:45 when they talk about the way patent holders get paid, "if anyone wants to use your wing design, they have to get your permission, pay you some money". The "get your permission" gets glossed over. The piece doesn't distinguish between "grant permission" and "get paid". That's a key problem because not only do giant, sclerotic multinationals hold back innovation to fit with their marketing plans, startups don't even try to compete (the goal is a buyout) and individuals are deterred from pursuing ideas because IP law is (for innovators, not lawyers) a giant pain in the ass.
So not only do you have to fight with lawyers (and pay them) in order to innovate, there's a very good chance that unless you are lashed to the prow of a multinational you'll never get to participate in the eventual product design anyway. So innovation is no fun unless you are already an IP lawyer. And by lawyer, I mean troll. So after innovating, in order to get paid or even make anything, you don't get to be an engineer any more. You don't even get to be in business in the sense of managing people and paying attention to the books, instead you have to do rigorous microeconomic analysis of markets to figure out how to extract all the consumer surplus out of the market you can. So the consumers don't end up benefiting much from innovation until after you lose your IP rights, but in the meantime you have new patents which continue your market control. It's the rentier treadmill, and worldwide it dwarfs even the financial sector for the inequality it causes and the long term damage to growth and human adaptability.
What if we separate the "giving permission" part (and get rid of that) from the "get paid" part? And by extension, once you give up the "giving permission" part you have to give up on the ability of patent holders to set the price for the "getting paid" part. That's a problem for patent holders, but not as big a problem if the method for getting paid is public, transparent, and balances the needs of market players who end up being both IP users and IP holders.
Very-high R&D cost industries (pharma, and according to an in-passing comment in the Planet Money piece, nuclear)
The folks who wrote the paper cited by Planet Money, "The Case Against Patents", talk about moving large R&D to the public universities and government research facilities. There's something to be said for that, but if we separate "getting paid" from "giving permission", then we can help with the R&D-intensive sectors by extending patent terms rather than contracting them.
Think about it: if patent terms are as long as one day, and those rights included the exclusive right to give permission and set the price, patent trolls (and sclerotic market heavyweights) are still empowered to wreak havoc in post-facto lawsuits against startups. Software, electronics, (and for those with their history caps on, aerospace), we're all familiar with the cases brought by and against RIM, Google, Apple, Microsoft, etc. It isn't the length of terms that's the problem, it's the fact that they include exclusivity for any amount of time at all.
Personally, I think we should normalize patents and copyright together at 40 years with some form of compulsory licensing. There's a symmetry to that. Copyright terms are too long, patent terms might be too short under a regime of compulsory licensing. It becomes neater that way, but I realize that copyright and patents are still pretty easy to deal with as separate issues.
Lawyers. They're in IP, and they're in government. If we threaten to get rid of patents, thousands of lawyers suddenly become very, very invested in completely stopping that change from happening at all. That's all there is to it, so any reform faces that immovable object. So the interests of non-innovating rentiers need to be taken into account. We can't get rid of patents, but we still give up too much economic growth and market churn under a regime of exclusive rights. We have to come up with something new, some kind of compulsory licensing. Lawyers should be aimed at each other, not at innovators and makers, so categorical prohibitions on using technology and information have to be replaced with marginal transfers from producers to IP holders.
What if we use the idea of open source to open a new channel in commerce? If a maker wants to bypass the current patent system, they have to put specs and source for what they sell online and put aside a set percentage of their revenue. Lawyers can trawl the online database looking for infringing products and file a claim against that revenue that has been set aside. Competing claims are adjudicated against each other and the maker never even has to talk to a lawyer, except maybe to ensure that their reporting is adequate and in good faith.
But the biggest problem will still be the rentiers and their shills going completely batshit bonkers about any reduction in their precious rights to control markets. They will be landing on this and similar threads like a ton of guano in 3, 2, ...