But as for the second part, I don't see any difference in coding efforts between jQuery and RightJS, if you really read the tests on github, you will see the size of code is about the same, RightJS is even compacter in many places.
I'd also like to note that it's quite nice that jQuery does not mess with classes directly, or with prototype. Although it certainly is cool to add additional methods there, javascript doesn't have a great way to namespace stuff added to global classes and makes it a pain when you mix & match other JS libraries into your project.
As for the safe mode, first of all it's not such a big problem as people usually think and actually provides more help than issues, and secondly RightJS will end up with a safe mode plugin sooner or later.
RightJS is extra careful with native classes extensions, it adds only standard methods and doesn't extend the Object.prototype at all. In many cases it's just adds missing methods in old browsers and that's it. And we always keep the original functionality intact.
We're trying to balance between the Prototype extensions hell and jQuery agnosticism. Things like String#endsWith, Array#compact is kinda standard features, they are extremely handy in everyday work and most of soberminded programmers won't hack those methods if they create some plugin that other people might use.
As the matter of fact most of jQuery plugins don't extend prototype too.
So it is a problem, but I believe it's negotiable and there might be a non-polar solution.