Like Syd, I'd say the combination of the PokéCenter and PokéMart are here to stayl. Going back to split buildings would be a step back for them [and us]. Although, that wouldn't be something new for Pokémon to do. But I see them remaining the same as they were in Black and White and B2/W2.
As for items, if I recall correctly, each generation has always added some more to what we can purchase. So, I think we're bound to see some extra items appear as well as new ones. I think evolution stones may be reserved for the larger department store, but I'd hope things like that will be found scattered amongst the region too ─ which they likely will be.