Are there are any notable problems or things to be aware of when introducing an ES6 to ES5 transpiler into a build pipeline?
Are these things mature enough for use in a commercial setting?
I have not had any issues with Traceur. You will not have access to the whole ES6 specification in Traceur (some features such as 'let' are missing) and some experimental features should be disabled for now.
The usual considerations when switching languages apply. ES6 feels a little bit like CoffeeScript in the sense that the language is not backward compatible. You can't just take a piece of uncompiled ES6 and pass it to someone running ES5 because you'll be using arrow functions and other unsupported syntax.
Traceur compiles to ES5, so IE8 is not supported.