Kalos didn't really have a department store because Lumiose City is essentially one. You have the pokeball shop, lotto id, berry juice, a high end boutique, stone emporium and the pokemon centers sold TMs.
Hoenn doesn't have a city with a scale as large as Lumiose. Hence, I still think the department store will make a comeback in Lilycove. Remember, the poke mart sells essential stuff but the department store also sell a lot of extras. They could forgo healing item purchases there and instead sell the regular TMs, pokeballs, furniture, clothes, boost items, X items etc.
As for Unova, the department store in the route seems really out of place honestly. I think it was put there at the very last minute... Or perhaps because there's not much exclusive stuff it sells, hence in that location. Hoenn, or even the 6th generation, has a lot more stuff which can possibly be exclusive to the department store.