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The nearest thing to this already is Linuxstep.
http://www.linuxstep.org/
I would comment on the article, but it's pointless as all the issues and their solutions have been thrashed out a long time ago.
The problem is that everyone has their own idea of the best possible distro, but very few can write code. Therefore we get a lot of wish lists, but very few real projects.
There are already countless 'ideal' package managing solutions, filesystem layouts, dependency resolving mechanisms etc, and to what benefit?
The 'innovations' are the *cause* of incompatibility not the solution!
OSX gets on perfectly well with /usr /var /bin /dev /etc, the difference is that apple understands the important part is making sure the user never has to deal with them directly.
You can rename entries in the root fs how you like, but if the <=average user has to navigate and comprehend them *at all*, you have already lost them.