I don't think this was done before, but ever since the "clock" was introduced, we had time-based effects based on the time of the day.
For instance, you can ride the Royal Unova in the evenings, and some pokemon only appear in the morning/afternoon/evening/night.
The most prominent effect was the evolution of Eevee into Espeon and Umbreon.
In HGSS, gym leader telephone conversations or photo taking was also available based on the date and time.
But pokemons aside - what about real-time effects?
For example, many shops are open until the evening, and are closed at night - just like the Valor Lake Restaurant.
Likewise, we can have citizen homes locked during the night so you can't visit them in the middle of the night. They'll re-open during the day.
Also, the number of people inside the house will change during the day - the kid would be gone during the afternoon to play outside and return in the evening. The family would be gathered around a table having dinner.
Same goes to work-places. While you might be enter the buildings, many of the clerks will be gone during the night, and return in the morning.
And in pokemon centers, there will be one or two people dozing on the first floor chairs at night. They'll move around in the afternoon.
What do you think? Will there be more real-time effects in-game for buildings/NPCs/shops/anything??
Edit: Pokemon Center/Pokemarts, Gyms, Villain HQ, anything directly related to the main storyline playthrough will operate 24/7.