Alright, just so people will stop repeating themselves here are the facts told so far:
1) Arceus and Shaymin are not in the internal coding of Pokemon Mystery Dungeon: Explorers of Time and Darkness
2) Arceus and Shaymin may appear in PMD 2
3) Arceus and Shaymin were not officially released upon the release of PMD 2, which is the reason why they are not in the game
Now then, please stop repeating these facts, I must have read at least five of number 3... Anyway, frankly, I don't think that those two would be mascots in any future game, considering they are technically fourth gen pokemon. Finally, PDM Blue Rescue team did not revolve around the mascots of Pokemon Ruby, Saphire, and Emerald because only the Groudon and Rayquaza were in the Main Story Line. Kyogre, on the other hand, was in Post-Story line. To be honest, I view a game to be finished when the credits roll, no matter what the post-story events are. Though I do aknowledge that the post-story was a good story, it is not the main game. Any questions?