'이'/'가' in ~ 이/가 아니다 is bojosas. So if I want to convey this nuance I will accent at the word 'NOT' in English.
'이'/'가' is also used as signifying subject in sentence, and in this case, it's not equivalent to whatever word in English.
'은'/'는' is for giving a additional nuance for emphasis, for contrasting things, for indicating topic.
을/를 is josa for objective case.