We do use r.js and create modules (a main one that gets download systematically, and smaller ones for less used features). However as we update often, we don't want our users to download the large third party libraries we use at each occurence, so having them as separate downloads is actually much better.

For the large libraries we use that are hosted on a cdn, with a local fallback, we use the :empty value for the optimiser and they are exclude from our modules.