1. Not a problem, though I don't use either, I tend to use very small modules (not necessarily via npm, but require'd in my own project, or outside modules)
2. React, and even the Yahoo flux tools are pretty nice. React by itself is less useful.
3. I'd go with es6-promise here, which complies with the spec. I wrote i-promise as a module to give an ES6 compatible promise library, or native as available.
4. Observables are pretty evil... the whole flux architecture is to avoid direct observations in favor of a unidirectional data flow.. but that's more opinion.
5. completely agreed... immutable data flows work to prevent side effects. Even if you don't use these libraries, avoiding side effects is a big thing.
6. Also agreed, though you can usually get the parts you want without the weird deep dependency chains in lodash.
7. Agreed here, though webpack is interesting, imho it breaks too much with node's approach to includes, and doesn't work as well with reusing code on the server-side (imho).
Other things to look into include csp, streams, events and the gulp build tool.