Oh wow. I just installed npm@3. This is awesome.
My node_modules folder now contains 582 folders, instead of 4, with thousands of nested, nested, nested, (and yeah guess it, RE-nested) crap!
This is the fix we have all been waiting for! No more long paths errors. Everything is awesome!
All in all, it takes all the dependencies of all your packages, and flattens them in the node_modules folder. No more nesting.
npm install -g npm@3 ASAP! (No idea if it's out of beta still, but I couldn't live without it anymore.