Well, yes. Certainly if we had a time machine, going back and ensuring a lot of the Javascript features were designed differently would be a major pastime (that, and ensuring the people who designed IE’s CSS engine never went into IT). But it’s not going to happen, and we’re stuck with it now.
I suspect, in time, it will become the “Machine language” for the web, with other better designed languages and APIs compile down to it (and cater for different runtime engine foibles).
I don’t think, however, any of these “better designed languages” will be Java, Python or Ruby. Javascript is, despite the ability to be used elsewhere, a Web application scripting language. Given that use case, we can do better than any of those languages.