First of all, npm 2's infinite nesting of dependency was a terrible design from the beginning. It was always broken (This is why on our windows build servers we need to do all sorts of stupid workaround to make npm work). There is no other decent package manager that nests dependencies within dependencies like that, every other package manager out there has a flat structure with packages and their version, so 2 versions of a same package can co-exist with no issues.

By fixing this huge flaw in their design, I thought there would be an increase in performance! In the end, they made it even worse. It makes no sense that fixing their flawed design would result in a 3x worse performance for doing the same task.