There's alot of evidence that they will, like:
'A Pokemon from Johto data' is programmed into the game. However, so is Plate for Arceus and Red Knot. Interesting, though.
G/S/C PokeBalls are present. The apricots are there too. You can't obtain them, they're just programmed in. Hinting?
But I honest to bet they'd be shit and would cut out some stuff, like going back to Kanto.