> For me the big difference is not between node/io.js for which a simple setting in your packages.json would be enough to sort out, but rather between es6 style modules and node style modules.
Setting the engine will separate things but this also means your package is now only available for that engine. npm doesn't give you a way to submit the same module multiple times to target different engines. So setting this limits the amount of environments your module. Maybe that's okay but the great thing about node + npm has been the ability to install and use any module you find; separating things would mean you'll come across modules you need and you might not be able to use. This kills the experience in my opinion.
> I'd probably rather have a separate repository for es6 style modules.
Why would you want one repository for ECMAScript 5 modules and one for ECMAScript 6? The end goal is to move everything towards ECMAScript 6 so would you want this to merge back into regular npm after a certain amount of time? Creating a different repository for modules that use language improvements seems like a bad idea to me. It's a good way to segregate modules from one another.