 <p>At the end I went with System.JS and jspm, and I must say it absolutely solves all the problems that I was facing, and then some, flawlessly. It took me a while until I finally found out about it, but I believe this is gonna be the defacto standard for a long while so I'd encourage anyone writing a new project to just default to jspm.</p> <p>You get AMD and Common.JS and ES6 support, you don't mix your node modules and client modules (node_packages and jspm_packages), and flat dependecies... what more could you need?</p> <p>Thank you for your suggestions!</p>