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They base it off Diamond and Pearl and don't do the Distortion World. Giratina's orb is hidden in the underground, which is now the focus of endgame as well as the way to find fossils
Spiritomb is a gift pokemon, the poketch is replaced by a pokenav with none of the functionality.
the elite fours teams aren't changed nor is the type imbalance fixed, Flint still only has 2 fire types.