tl;dr: "We want to build isomorphic apps, so we wrote a new package manager"

Coupling the goal of building isomorphic apps with the need for a new way of managing packages to accomplish that goal doesn't make any sense. How you install packages and manage dependencies has absolutely no bearing on what you can or cannot do with those packages.

In other words, you can write fully isomorphic apps using npm as your package manager. We're already doing it.