I prefer straight JS over CoffeeScript/TypeScript/Flow etc...
I don't find require/modules to be too much of a mess.. unless you are using a lot of really large tool-chains with deep dependencies... npm dedupe helps point out problems there.
Breaking your logic into idempotent functional components without side effects as separate files/modules reduces a lot of what can be considered ambiguous or unexpected.
If you work with a functional flow, avoiding OO in JS as much as prudent, you can get a lot done without nearly as much confusion.
For now co/generators/promises get you really far along. In the future await/async will take it farther.
> Facebook Flow or TypeScript - still weak.
How is it weak?
On require/modules, that's a freaking mess.
Ambiguous/unexpected behavior... nothing fixes it.
To make matters worse, there's always the promise of some magical library or tool that's going to fix your problems, until you discover that it sucks, or that it is unmaintained, or that it doesn't interoperate with another library and then you're back to search between thousands of pieces of crap that do the same thing.
I remember the days when people were having boners over CoffeeScript. Boy, that was a bad move.