Personally, I’m not such a fan of Webpack. It trips my “too complicated” alarm, like RequireJS before it. I’ve never worked on a project that needed the kind of dynamic behaviour these tools support, and you pay a price for that flexibility in the complexity of the tool and the output it produces. Likewise, while you can include almost anything as part of your bundled JS output with Webpack, I’ve seen few real world cases where this is a significant advantage, and again you get locked into Webpack and its complexity as the downside. Perhaps on some types of project the features Webpack offers represent more compelling benefits.
For perspective, I’m also not a fan of tools like Gulp, also on the grounds that their ecosystems tend to be fragile and they add unnecessary complexity to what is usually a pretty simply operation in the first place.