Many political figures at the time felt representation in Congress should be based on the amount of free men each state had and their "quota of contribution". Notably, James Madison drafted the Virginia Plan with this proposition in mind. States with a large population (Virginia being the biggest at the time), would therefore have more representatives than smaller states. Naturally, large states backed up this plan, while smaller states were against it.
In the end the issues were settled on the Connecticut Compromise, which ensured the creation of a House of Representatives apportioned by population, and a Senate in which each state is equally represented.
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