My advice has been the same from the 1995-ish days of RH... you need a solid foundation that is close to static and stable to build on. Just like the kernel, there cannot just be chaos. Linux needs to be not just the kernel but the basic framework and a single set of core apps. Instead of 15 terminal apps, window managers, editors, etc. There needs to be one, and the very best/stable/simple one from each category. This would get people interested in working on that one project since it would bring the most fame and notice, it would make the base system close to a standard, and it would eliminate a lot of complexity. From there people can be free to add whatever they want in any of those categories or specialized apps but the foundational base would still be standard. That alone would be huge.
After that my opinion is that there should be self-contained applications. All the files and dependencies should be in the apps package and directory. With disk being cheap and huge the redundancy and extra space would be completely worth it to give up. It would make the dependency hell go away and it would simplify so many aspects.
After 17 years though, I'm not holding my breath... the usual crew will just continue to say how it isn't necessary and go about their business with no regard for reality.