I\'m currently using System JS with System JS Builder to bundle up my application, its assets, and the libraries that it references. My problem is that I can bundle librarie
You can use a bundler like Webpack or Rollup (my preference because it does tree-shaking).
The Angular team appears to be putting together some great tooling around Rollup in time for the full release. The day 2 keynote of ng-conf this year discussed and demonstrated the offline compiler. Start watching this at 25:30.