There are also other problems such as nesting functions inside other functions inside other functions which is IMO much harder to maintain than a clean flat list of functions defined in the prototype. Don't even get me started on using "self", "that" or "me" instead of the built-in keyword "this".

It could be just me but I cannot understand how that was/is/has been acceptable at all in the first place. Doesn't functions nested 11 levels deep (true story) ring any alarm bells for people?