There is the theory that Shaymin will be available in the inevitable G/S remake (though not without an event to give you Oak's Letter to unlock the event), because of the way Prof. Oak is involved and mentions there being something similar in Kanto. It's possible that Shaymin's appearence in D/P is there to either match up with a similar event in the remakes or even just there like Deoxys, Lugia and Ho-Oh were available in Emerald, despite the events for them all being aimed at Fr/Lg.
If this is the case, Arceus can probably be expected to be unlocked at the time of the third game to D/P. It's possible, even, that this game wont be a counterpart game to D/P but rather a sequel. Team Galactic are still functioning after their defeat in D/P, and though it's never referenced by name, Cyrus is obviously only going after Dialga/Palkia to get his hands on Arceus - which will grant him the power of a God that he desires. Arceus' event is even started at the same place atop the Coronet Mountains.
Who knows, Arceus might even be obtainable in game.