Sadly the users most likely to be inconvenienced by a change like that are also those with the least knowledge of the product(like if you don't know what babel actually does, you aren't going to understand why the cli stopped working or why you need this new config file to make it do something). That leaves them frustrated and angry but with a poor understanding of why and what adequate solutions would be. There is nothing you can do about that, asking the community to be nice isn't going to help because most of your users don't think they are even in a community.

The only things you can do are try to anticipate them a bit, and to try and count the criticisms but ignore their contents(and search yourself for the deeper cause). Luckily the first part is sort of easy for JS projects because most of the active tooling development in JS is on things that have been done many times before. In this case you could have just looked to gcc and wondered for a bit why they still ship with --std=gnu90 by default, despite how maddening that must be for all the developers working on new features that go underused as a result. You could have looked at all of the other software that is stuck dragging forward dumb configuration systems with complicated defaults and layers of precedence instead of just asking users to fill in a few config fields on first run.

So I do want to say that I am so sorry on behalf of your users, and I really appreciate the work that you do. However that was a real mistake with babel and a big part of improving the interaction between you and your users unfortunately falls on you.