So if the sprite is a Youngster, School Kid or Preschooler, then it could very well be him. But it could also be a reference to the Patrat Lady from Unova.

The kid uses the Preschooler sprite, I believe. And yes, it is probably also a reference to the Unovan Patrat Lady. Which is a curious coincidence; I remember prior to XY's release, some people were thinking that the Holo Caster on Tierno's wrist looked more like an Xtransceiver, and inferred from both that and the Vanillite design on his shirt that he could be from Unova. But, that is just coincidence.

And just because the Grunt who taught the girl the song was wearing a red suit doesn't mean he was part of Team Flare at the time. In fact, Flare's suits are orange, not red. So he could've been wearing red clothes when he met her.

Team Flare's suits are described as red in the games (ex., one NPC says, "Are red suits the hot new trend?" referring to Team Flare; I seem to remember some other instances but cannot recall them offhand) and on the official site ("You can easily recognize Team Flare members by their brilliant red suits."), but even setting that aside, the "red clothes" descriptor is supposed to fecall to mind a Team Flare grunt, I would think.

And don't forget Zinnia's connection to AZ

I was not aware of a connection between them. What is it?

Archie and Shelley's connection to Jirachi

Ah yes, that is another good one that I had forgotten about.

Looker to both the Battle Resort and Xerosic and Malva

These are a bit more than an "implied reference," though, no? More of a minor cameo in one game and a full sub-plot in another.

While we are discussing the more direct references/cameos, however, I suppose I could also throw in Kiyo/the Karate Master setting up a Fighting Dojo disguised as a dance studio in Lumiose City. Also, there is Inver, who seemed to be running a business centered around Inverse Battles in Mauville City back in ORAS, but then I guess he retired to Kalos many years later?

Colress with Route 10 and Blue Oak with Lumiose City.

Those two are both mentioned by name, though, which is why I didn't bring them up. Although the reference to Blue does interest me in another way. The woman says that Blue came to Kalos to study abroad, and that he "got 'Bonjour' down just fine, but still always said, "Smell ya later!" when he left." This strikes me as a reference to him greeting you with "Bonjour!" on the S.S. Anne in the Kanto games. So, I wonder, did his trip to Kalos occur back when he was very young, before the events of the Kanto games? I guess it seems a little odd that a ten-year-old would be studying abroad, but then, this isn't our world, and he is the spoiled grandson of a very successful Pokémon Professor.

Another one that I remembered just now is the Mirage Spot rings. Obviously, they were conjured by Hoopa, but aside from the visual similarities, the games don't ever directly connect the two.