Why did the Persians chose to destroy the acropolis instead of any other building?

The Persians burnt down Athens including the foundations of the new Acropolis being constructed as payback for Marathon after Persia tried to invade Greece to gain more territory and was defeated.

The Athenians had previously helped the Ionian Greeks of the Greek city of Sardis, revolt against the tyrannical satrap of Persia and Persian subjugation in which the Persian temple of Cybele was burnt down. The Ionian revolt delayed Persia's attack on Greece and fuelled Persia's lust for more and more land. Xerxes then used the revolt as a pretext to invade mainland Greece.

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There was a group of hold-outs defending it and there was also payback - the Athenians had earlier been involved in the looting of the Persian provincial capital of Sardis in Asia Minor, where they destroyed the statues of the gods. But they wanted the city as quarters for their army.