The problem is not necessarily starting a new project if a full rewrite is needed, but rather the persistence of multiple redundant implementations.
In the case of Linux, it has no competition as an open source kernel.
On the other hand, there's no reason to have multiple packaging standards, yet .rpm and .deb persist with significant market share each.
The fact that the dpkg and RPM maintainers don't get together and kill at least one of them is a true disgrace, and is one of the things that holds back GNU/Linux from being more popular (note that they could always flip a coin if they can't do anything better).
That's just one of the most glaring examples, and there are many others like upstart vs systemd, gtk vs Qt, desktop environments, gecko vs webkit and so on.