Well, Arceus and Shaymin weren't officially released before PMD2 came out. I'm betting that PMD3 might deal with these two or Giratina since the PMD games seem to revolve around their generations' game mascots.
It could also be that they may be released in some sort of special mission on the game, similar to how they have the special Shaymin mission on Ranger Battonage. I don't know, but since they are part of this generation, that would seem most logical really than them appearing in a PMD3.
Arceus might be the big boss of PMD3 if it comes out....I find it to be a drag that the two aren't in PMD2 myself....actually...Arcueus I can understand cause it's a God Pokemon...Shaymind, on the other hand...all it does is create flower fields...so...eh...I dunno.
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?
Perhaps there is a way that they can update the coding, like how you update computer program. But it would make sense for them to appear in a new game. Unfortunately, unless a 5th gen comes around, there's really no reason to make a new game.