"Your aunt is the sister of one of your parents."
Translation:Via onklino estas la fratino de unu el viaj gepatroj.
"De" is used when you can replace "of" by 's (someone's sister). "El" is used when you mean "elements of some set". Here a parent is an element of the parents set.
Well, the usage of de is unfortunately much more broad and inconsistent than that. You'd think Esperanto would've been given a different preposition for each different meaning of "of", but alas even Esperanto is based off of some mutual expectations here and there. Calling it a "neutral language" is an overstatement; it's full of flaws and idioms that simply result from its being based off of solely European languages.
Usage is more broad. It can express many other relations which can be desribed in many manners. So if something is not clear maybe somenone don't express thoughts clearly.
Yes, but usage corresponds to definition. When a word like de is assigned a broad range of meaning, it's not the speakers' fault for using that range of meaning.