I think Webpack is a step in the correct direction, but web bundlers are still in need of improving.
Maybe I was doing it wrong but for a previous project I was using SystemJS for module loading + bundling and Gulp for SASS + TypeScript compilation and livereload. I've replaced all of this with a much simpler (before I had too many differences between development and production builds) Webpack configuration that does everything. Setting up both configurations drove me up the wall with the usual array of "module not found" and "file not found" problems you have to persist with but the Webpack setup feels more robust now that it's working.
Probably not an easy problem, but it would be amazing if build tools by default gave you a lot of help with debugging errors e.g. "module a/b/c not found, did you mean ../a/b/c?".