Yep, NPM is transitioning to flat in V3. Partly because of the nested folder limits in Windows, partly to reduce the ridiculous amount of dependency nesting that occurs with the current model.

JSPM already uses a flat dependency structure. If you look at how it maps dependencies (and specific versions of dependencies) in config.js it makes a lot of sense. The only feature it's missing is the ability to easily search and list multiple versions of the same dependency.