HTML Imports are going away. I'm not sure the state of Polymer but my guess is that they will be removed eventually, so I wouldn't depend on a tool like Vulcanize being improved; it's a dead feature.
Instead use a normal JavaScript module loader to load components and concat them the usual way. Don't use imports.
HTML imports allow you to bundle HTML, CSS, and Script and import them in one step. ES6 only handles the script part. We very much love HTML Imports on the Polymer team and they aren't going anywhere for us.
I expect that when the ES6 modules loader spec is finalized it will be fully compatible with the underlying semantics of HTML imports, and they will work quite nicely together.
There are several competing proposals for asset imports [1] any of which are viable. HTML Imports may persist, be supplanted by ES6 imports, or may otherwise survive in a different but similar form. Hell, I wouldn't be surprised if one day someone makes a web component to implement the current HTML Import spec using whatever the browser happens to support.
Instead use a normal JavaScript module loader to load components and concat them the usual way. Don't use imports.