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The detail of some of the cities.
Flomora Town and it's field of flowers, especially its little path it had so you didn't walk on any of them
Slateport, with its beach, lighthouse, museum, dock, and especially the open market. It's my favorite town. It's just very real; like a town that you could see being in our world.
and Olivine:
from the detail of the ground tiles, to the board walk, to the picnic tables, to the ships docked there, to the lighthouse, and the different shaped/colored house, the fences around the grassy areas
and especially the flags around the town that move in the wind.
I always love the cities near the water because they have the most character it seems.
Also, the faceboards in Pastoria and Humilau cities; and the fact that they get used and aren't just "there".