B - Incorrect: This option does not have a clear grammatical antecedent for the pronoun it.
C - Incorrect: This option does not have a clear grammatical antecedent for the pronoun it.
D - Incorrect: The usage of what was is redundant in the presence of the past simple was.
E - Incorrect: The usage of the past perfect tense had been is incorrect because the sentence does not put two past events in sequence. Additionally, this sentence implies that Aquincum was a nickname or alternate name for Budapest, changing the meaning of the sentence.
A - Correct: This option correctly and clearly conveys the meaning that Budapest was Aquincum. The pronoun it correctly substitutes for Budapest.