Rollup looks nice too. As far I understand rollup, it's generating more human readable and shorter bundles, so it's more suitable for libraries. I didn't tried it yet, but I feel somehow that if I do, I will find bad parts there too. Like limited (comparing to webpack) module format support...
Yeah, it's pretty common (for the tree shaking case) to make a custom d3/whatever library bundle with Rollup and use it with Webpack for your app, but it's a formidable alternative to Webpack regardless.