In Pokemon Mystery Dungeon Red and Blue all Pokemon from Generation 1, 2, and 3 were in the two games. Generation 4 was hinted in the game by the Lucario, Bonsly, Mime Jr., and Weaville statues. That generation was not in the game because it was not released yet. In Pokemon Mystery Dungeon Explorers of Time, Darkness, and Sky they went up to Generation 4 because generation 5 did not exist yet. In the WiiWare PMD, all pokemon up to Generation 4 were available but there was a trick. The three games each had up to 130 version exclusives so in order to obtain all of them the player needed all three games. Overall, every PMD game has had every Pokemon in its data and each set has had the oppertunity to "Catch them all" in a similar fashion that each generation of the main games has. I realize that Chunsoft develops it but Nintendo publishes it so I would still be disappointed in them On the brightside, here is a new trailer!
http://www.youtube.com/watch?feature=player_embedded&v=PVdNnbw2gts" frameborder="0" allowfullscreen>
I saw Umbreon, Espeon, Marill (or Azurill not quite sure), and Jolteon all in the dungeon which is good news for all Pokemon being in the game :D