Alexander18
Dragon Pokemon fan
As far as I know that seems to be open ended dialogue that doesn't result in anything.
I almost wonder if that was also intentional. The Delta Episode was obviously a way to integrate Rayquaza into the game's plot without having it take the spotlight from Groudon/Kyogre during the main game (hence no Emerald plot), so the Delta Episode would naturally make Rayquaza the star of the show during post-game. If we didn't know about Deoxys that would have been the most exciting part and would probably cause Deoxys to get in the way of Rayquaza's limelight more, which could be something they wanted to avoid. That's just conjecture though and I'm possibly just looking for an explanation where there is none.
I would prefer the Emerald plot in the game than R/S plot, Emerald plot was fantastic and seeing Kyogre and Groudon fight and Rayquaza coming down the sky to stop them was the best bits from the Hoenn region game. I don't see how Deoxys and Rayquaza are connected in any way and the fact that these games are based only on the originals with no elements (such as the battle Frontier) from Emerald was the biggest con of these games. I don't see why they made Deoxys available considering that mythical pokemon are not allowed to be caught in the games.