I'm just writing a first React app, and read beforehand that it was going to be difficult to choose which libraries to use, and to get them to work together, but I haven't found that to be much of an issue in practice.

create-react-app set up all the build tooling, for a router the clear recommendation is react router, and for a flux implementation the clear recommendation is Redux. It feels like there's a well defined path for beginners. Over time you'll have to figure out how everything works, as is always the case, but you can learn more as and when it's necessary.

The bumps were more whether to use ES5 or ES6 (but then I found an official position in favour of ES6), and whether or not you need to use flux (although that was really just learning how flux worked, which wasn't wasted time).

The only uncertainty I have now is whether TypeScript will be necessary/useful in future, and if so how to integrate it.