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Japan is living in the future that the 1990s dreamed of.
(startrek.website)
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Rebuilding everything from scratch will take ages and cost everyone a lot of money, because you have to replace all your hardware (router boxes, PC s, phones, smart watches, ...), because the internet protocols are often designed into the hardware itself, and changing them fundamentally means a lot of trash. Also there is no system that guarantees that the result will have fewer issues or will not required to be succeeded by something else a couple of minutes later, because some new issue was discovered.
Also software is highly complex and need to adapt to many different scenarios, while maintaining compatibility to each other, which the other disciplines of human engineering don't have to deal with as much, they are much more purpose driven.
It is like trying to create a universal building code (for building houses) that simultaneously works on every country on earth, hell, maybe even on multiple planets, with wildly different and constantly changing environments and is guaranteed to result in save houses. Not really possible in one shot, only possible by constantly trying to adapt. That is what software has to deal with. I am talking about fundamental software like the Linux kernel here, for example.
You cannot just start over and be better.