There are many different reasons. But one explanation is that the three matzot represent the Cohen, Levi and Israel. In that case the middle matza is the Levi. The tribe Levi in Egypt were not slaves. So they suffered less, therefore we leave only a small part of the tribe’s matza on the table. The bigger part, is the afikoman, is removed from the table during the reading of the haggadah.
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