So I've gotten to Team Aqua's base and wandered in (I assume) Shelly's room, and found a picture with the following text:
There's a picture of a boy with a shaved head, a girl with black hair, and a Pokémon with three notes attached to its head.
"The 7th day of the --th month, --002.
With Arc--e and --rachi"
The letters at the edge of the picture are faded and hard to read
I assume there is similar text in Omega Ruby in Tabitha's room.(apparently there isn't)
"Arc--e" is obviously Archie, the black-haired girl is Shelley, and --rachi is Jirachi, the Pokemon with "three notes" on its head. "--002" is probably a reference to the year 2002, when RS first came out.
I'm not really sure what to make of any of this, after all, why mention Jirachi at all? They included Deoxys as an in-game capture, and people are speculating on DLC. What if the DLC packs for future Pokemon games come in the form of "episodes" you play through, much like the Delta Episode and unlocks features associated with the DLC (e.g., after the Jirachi episode, we unlock the Battle Frontier).
It seems like a really weird reference to be making either way, especially since there isn't a Magma equivalent, making this a very strange disparity between games.