Not really software but, personally I think the FHS could do with replacing. It feels like its got a lot of historical baggage tacked on that it could really do with shedding.
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Wayland could already do with a replacement.
Seriously, I'm not a heavy software developer that partakes in projects of that scale nor complexity but just seeing it from the outside makes me hurt. All these protocols left-right and center, surely just an actual program would be cleaner? Like they just rewrite X from scratch implementing and supporting all modern technology and using a monolithic model.
Then small projects could still survive since making a compositor would almost be trivial, no need to rewrite Wayland from scratch cause we got "Waykit" (fictional name I just thought of for this X rewrite), just import that into your project and use the API.
It is so much better than X
dmesg
/jk