Agreed. It's frightening to see people embrace web components while completely ignoring the usability issues, and adopting the attitude of "develop first, think about API design later."
The folks behind web components are super open to feedback. I'd be happy to introduce you so you can provide some feedback on where the spec should go to better address the pain points you have.
Do you know how they'll tie into ES6 modules? (if at all), that's definitely a big concern for me, I'd like to never see a global again as far as libraries go. Anyway yeah that would be great! I totally understand the end goal of having something usable out of the box, I'm just not 100% convinced browsers can even really get away with that. There's still fundamental issues like dependency mapping and manifests etc that are purely user-land anyway, so at the end of the day they wouldn't really be useful without some sort of registry/packaging mechanism anyway