Javascript has problems. If it didn't, no one would be trying to evolve it and address it's weaknesses. The language had serious weaknesses, some of which were addressed recently (TypedArrays, strict mode, etc) and some of which there is no current fix (consistent, standardized, namespacing and modules), and some of which cause big performance holes ("with" statement).
Prototype based inheritance is extremely verbose to use. That's one reason why CoffeeScript is well liked, and why Classes are coming to JS. Prototypes and eval() also make it hard to develop language analysis tools and IDEs which can provide correct code assistence, which can refactor large code bases, etc
Javascript isn't broken if you're just writing a few lines of JS in jQuery to enhance a web page. But it doesn't really scale well if you're got 500klocs of code and a decent sized distributed team.