Are there debuggers that can single step over the transpiled bits so that it feels like the methods are implemented natively? Otherwise, it becomes a mess.
With the right debugging tools, transpiled alternatives to JavaScript are easier to debug than vanilla ES5.
For example: TypeScript's sourceMap [1], Elm's time-travelling debugger [2], Vue.js DevTools [3], just to name a few I've tried. Especially well-typed languages tend to behave well at run-time once they pass type-checking. Or rather, I have not made enough front-end code to discover transpiler bugs.
Because debugging better languages affords you more context and more tooling.
Elm's debugger lets you step forwards and backwards in the application's state.
TypeScript's type system lets you catch bugs before you run the code.
Vue.js's DevTools extend the browser's with a component-based overview, so you can interactively see what's going on at a high level of abstraction. (I'm sure something similar exists for most frameworks similar to Vue.js, and possibly even frameworks made in vanilla ES5, I'm just picking one I've tried.)
I started with your position (vanilla js 4ever!) and after being dragged into the world of transpilation via typescript/eslint/prettier/webpack/babel/etc I do agree that it’s at least as easy. Not sure about “easier” but my debugging needs are not exotic. The painful part is initially setting up the toolchain.