I've been using Typescript in my current angular project for about a year and a half and while there are a few issues with definitions every now and then the DefinitelyTyped project does an amazing job at keeping up with the latest versions of most popular libraries.
If you plan on using angular 2 there are a lot of examples using TS and I think the team will continue to provide most of the documentation in TS, but you certainly don't have to use TS to use angular 2.
ES6 does have some nice features and I personally plan on getting more familiar with it but I would not consider it a production ready language at this point. Mainly due to a lack of support by current browsers. See this SO answer for more details. Of course you can write you code and ES6 and use a transpiler to get it to ES5, which seems to be the popular thing to do right now.
Overall I think the answer would come down to what you and your team are comfortable learning. I personally think both TS and ES6 will have good support and long futures, I prefer TS though because you tend to get language features quicker and right now the tooling support(in my opinion) is a little better.