Well, to clear any confusion about the whole Hoenn thing, they most definitely will not be putting it in. Why? Well first, memory and all that claptrap, the card won't be able to accomodate three full regions, guys.
Second, they're putting Kyogre and Groudon in because there isn't going to be Hoenn. Because of the DSi, GBA game compatibility has gone out the window, so they're putting Hoenn legendaries in so that the pawr baaabeez who have a DSi will be able to get them without having to rely on trading. I wouldn't be surprised if Latias and Latios were released as event Pokemon sometime, either.