How was the final draft of the Constitution different from the Virginia Plan?
The construction of Congress feels like it could be the most significant difference between the Virginia Plan and the enacted Constitution.
In the Virginia Plan, the lower house of Congress (House of Representatives) would be elected by the people of the states, by population of a state. Much like today, a more populous state would have more Representatives.
The difference is that the Virginia Plan would have had the Representatives electing the Senate, rather than the legislatures of each state. In other words, larger (i.e. more populous) states would have had significantly more power in Congress than they do under the Constitution, which originally provided that the state legislatures would each elect two senators, irrespective of state population.