I think FreeBSD, and the Linux distributions do try to cater to too many different people, and quality and coherence suffers a lot from this. I think we can get past this though. The culture of testing and good code is on the ascendant again in many quarters. You need more people to understand build, packaging and distribution better, sure. You also need autotools to die, as the use cases for it are mainly dead. You can generally write portable code to the systems that matter if you want to now, and it just works.

A lot of the problems are due to poor integration between languages, so for example the JVM people have reimplemented almost everything, as have the C++ people.