There was a major disagreement among the state regarding the system of representation under which Congress would operate. The creators of the New Jersey plan supported a system in which every state had 1 vote. This favored the states with smaller populations over the interests of states with larger populations. The creators of the New Jersey partially supported many contents of the Articles of the Confederation. This is why they proposed an amendment to it rather than a replacement.
The plan was ultimately rejected as a whole, as the Virginia Plan, proposed by James Madison, was ultimately adopted. However, many of the contents of the New Jersey plan would eventually be taken into consideration during the Constitutional Convention.