2) I felt the same way for a while, but recently I was working on something where I ended up really "abusing" the prototype system, and when you actually spend the time to learn it, it's not that bad! It's different, that's for sure, but it's not bad.
I like to think sometimes that if javascript came before C, would we still call many of these things "bad"? Would we call javascript's equality table "weird", or would it be C's that was the weird one? Would C be the star in a talk labeled 'Wat' where they laugh at the absurdity of 'a' == 97? So much of the stuff that people complain about in JS is because they have expectations from other languages. Sometimes those expectations are a good thing, but other times they are just different, and taking the time to actually learn how and why it's different can make you a much better programmer.
3) I genuinely like this about JS. There is no "one true way". The language is free to evolve, change, get new features, get new functionality, and easily "polyfill" old browsers outside of the release cycle. And that's important in JS because there is no one "authority". Keeping the stdlib small means that it's easier for new implementations to crop up, and it leaves the "niceties" to be developed by libraries. It's what allows libraries like ramada and lodash to be so powerful. They wouldn't be where they are today if the stdlib was more opinionated/complete.
4) But again I kind of like this. It does often make things more difficult, but at the same time it improves the ecosystem. I honestly believe that the fact that there are competing implementations is pretty much the only reason javascript (and in some ways, all dynamic languages) are as fast as they are today! Not only that but the fact that there are multiple competing implementations keeps most devs "honest". For the most part I don't need to worry about someone writing code that will run on version X on platform Y. I don't need to worry that the next "update" will require us to spend a week cleaning up removed functionality. It does lead to a lot of "crap" accumulating in the language, but over time that crap can and will be removed. JS is a fluid, constantly-evolving language, and because of that you tend target a point in time, not a "release", and the impressively awesome backwards compatibility means that while your older code might look outdated, it's not going to suddenly stop working.
I do agree that complex JS programs need much more tooling to be manageable, but it's working out very well in my experience. It's just different.