Nice to see some actual numbers and research on the topic. Most complaints about NPM seem to fall into the category of fretful, emotional hand-wringing (although there's some of that here too).

If we measure success by the amount (not the percentage) of high-quality packages available, NPM is easily the best package management ecosystem yet. But there's definitely room for improvement.

One major improvement I'd like to see is some solution for unwanted indirect dependencies. If I depend on package A, and A provides features X and Y, and I only need it to do X, and the code for doing Y depends on package B, then it shouldn't download B. The recommended solution is to split up A into a family of packages (like lodash's per-method packages), but that just creates a mess of versioning that's annoying for both the authors and the consumers. And those massively-multipackage libraries (like Babel) just seem to create dependency hell situations that semantic versioning is not good enough at solving. So maybe instead of package splitting, the next-gen package manager could have first-class understanding of ES6 modules, with tree-shaking logic to prevent unused indirect dependencies.