This was done for the purposes of representation and taxation in the lower house of Congress, not presidential elections. The smaller States believed that unless they had equal representation the large States would dominate Congress and legislate for their own common benefit and interest. The FF's figured nobody besides George Washington could win a clear majority in the first presidential election, in which case the election would be decided in the House of Representatives, where each State got one vote. They further predicted that each subsequent presidential election would ultimately be decided similarly.
The FF's did not create the E.C. to solve the problem of how to count slaves towards presidential elections. The FF's failed to predict the rise of political parties.