Agreed as well. In fact, I would posit that this wasn't even really a problem until npm@3 came out and made installing dependencies far, far slower. Yet it was necessary; a standard project using babel + webpack installs nearly 300MB (!!!) of dependencies under npm@2, and about 120MB under npm@3. Both are unacceptable, but at least npm3 helps.
I want to plug ied (https://github.com/alexanderGugel/ied) here, which both installs about 5x faster than npm@2, yet deduplicates as well as npm@3.