Eu sugiro que você leia este artigo que, na minha opinião, explica muito bem por que estender objetos é uma má idéia, no que diz respeito ao Prototype também.
Falta de especificação
Exposure of "prototype objects" is not part of any specification. [...] In order for implementation to conform to DOM Level 2 fully, there's no need to expose those global Node, Element, HTMLElement, etc. objects.
Os objetos de host não têm regras
DOM objects are host objects [...] Host objects may implement these internal methods with any implementation-dependent behaviour, or it may be that a host object implements only some internal methods and not others.
[...] Internal methods behavior is implementation-dependent. [...] By definition, you are working with something that's allowed to behave in unpredictable and completely erratic way.
Possibilidade de colisões
Given huge amount of environments in use today, it becomes impossible to tell if certain property is not already part of some DOM. [...]
Every named form control shadows properties inherited through prototype chain. The chance of collisions and unexpected errors on form elements is even higher.
Employing some kind of prefixing strategy can alleviate the problem. But will probably also bring extra noise.
Sobrecarga de desempenho
[...] browsers that don’t support element extensions—like IE 6, 7, Safari 2.x, etc.—require manual object extension. The problem is that manual extension is slow, inconvenient and doesn’t scale.
[...] once you start extending elements, library API most likely needs to return extended elements everywhere. As a result, querying methods like $$ could end up extending every single element in a query.
O IE DOM é uma bagunça
As shown in previous section, manual DOM extension is a mess. But manual DOM extension in IE is even worse [...]
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