I'm in the camp that Babel 6 was "useless by default" in the bad sense. It's great that when you use tsc you know exactly what features are supported or not, and don't have to change anything, or worry about compatibility between things. And I'm starting to all the babel-preset-* packages have just created a bunch of busywork for the maintainers.
Then there's the issue of tooling requiring Babel. react-hot-loader should not require Babel. graphql tooling should not require Babel.
I'd argue when you're knee-deep in Babel, you're no longer writing JS, you're writing BabelScript. Only your BS capabilities are different than Jane's BS capabilities, which are also different from Bob's setup over there.