There's even a pull request to bring typescript into the mix. https://github.com/facebookincubator/create-react-app/pull/5...
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.
It was very promising at first but typescript now has caught up with Flow best design decision: noImplicitAny, strictNullChecks.
Also, check on the "try typescript" website: typescript's JS output is almost left untouched. it's effectively a replacement for babel, if you only care for ES2015 stuff, and not some of the more recent stage 0 / stage 1 stuff.
The issue is that TS 1.8 doesn't support async/await in the browser until v2.0, but a ts -> babel transpile does the job nicely.
It was made for demos, proof of concepts, and beginners (at the beginning, maybe not anymore). I don't know how Angular CLI works, but if it works like Ember's, then there's no comparison. Ember CLI generates models, controllers, etc. any kind of thing and it enforces a file and directory structure that makes all Ember apps look the same.
I know a lot of work has been put in to angular-cli and it's been through a few iterations at this point, but I almost wish they would scrap the whole thing and fork create-react-app.
