Question

why the structure set up by the Great Compromise is still in effect today while the structure established by the Three-Fifth Compromise is no longer in effect.

Answer 1

The Great was retained because it merged proposals from large states and small states about congressional apportionment. Eventually, the main contribution was in defining the apportionment of the senate, and thus retaining a federal character in the constitution. It was proposed that the proportion of suffrage in the 1st. branch [house] should depend on the respective numbers of free people.  It added that for the second branch or Senate, each State should have no more than one vote.  Though this plan failed it was finally resolved and an amended version of this plan was included.  Benjamin Franklin made modifications so that each state big or small was represented in the senate.  The Three-Fifths Compromise was no longer retained because it focused whether or not to include slaves in the total population count and victory in the Civil War ended slavery making it null.