The main issue that I see with that transition is that nothing in Brunch prepares you for the abstractions that Webpack uses. I think with Webpack the important thing is not to be afraid of the configuration files. After being used to tools that exclusively use JSON for configuration, working inside a CommonJS module that can dynamically assemble the configuration object seems a bit strange. But as you are assembling more and more powerful configurations, you tend to develop the skill that comes in handy outside of Webpack - writing Node.js glue code.
Whenever there is a job that isn’t covered by Webpack and that other tool still has a gimped CLI (i.e. npm script is not enough), you still have the fallback of cobbling together a Node.js script that does what you need to do - without necessarily escalating to Grunt/Gulp and hoping there already is a usable plugin (or having to write one yourself).
Now if you are doing a lot of esoteric stuff, Gulp’s infrastructure can be helpful in the long run to get away from the nitty gritty of developing Node.js scripts but I’m not sure many people would actually get a sufficiently high return on their Gulp investment.
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