I've been wondering why Linux distributions all end up being Unix-like, but I suppose it's obvious. Compatibility, and that fortune that goes 'Those who do not understand Unix are compelled to reinvent it... poorly.' And who really understands Unix?
I'm occasionally tempted to implement a distribution which keeps its packages in packages (much like the nextstep/macosx 'bundles') and has a shell that can find stuff in them. It should be easier to deal with upgrades and version skew this way. The problem is that I don't know what bits will be harder this way.
init is another candidate for reworking. It won't start daemons for ordinary users, it spawns some things from inittab and some from the init.d scripts... It's all terribly ad hoc, I feel.