This depends a little on what you plan to do with your node-fu.
If you plan to learn a bit more, maybe work on your personal projects or start something new in a new company, then I think you should just start with Node 4 (the TLS version) and write "native" ES6. Even if you're just learning at the moment, you can still go on and learn, because most of the time the transpiler is set up only once, at the project start, and then you forget about it.
And if you plan to contribute to older codebases etc, you can just add the transpile step later, and you're done.
But if you plan to go work in a company already using node, or publishing libraries that you expect will be widely used, be aware that a lot of companies still use Node 0.10 and Node 0.12, and those apps will be around for a long time. So working on something like that might even mandate the use of ES5 only, without even transpilation.
So TL;DR would be, just write ES6, worry about transpilation when you have to.