The Pokémon Mystery Dungeon Adventure Squad series is unique in that they are three games on a Home Console. As they are on the console and not on the handhelds, connectivity between versions is done in a completely seperate way. Instead, the majority of the game's cross compatibility comes from having all of the versions on the same Wii.
With this, you can utilise the same save file in order to have your progress tracked in all three games.
Unlike the previous multi-version Pokémon Mystery Dungeon games, the dungeons in these three games are completely different. Each dungeon has a general theme that spreads across the respective dungeons in the other versions, but the Pokémon within each dungeon is completely different. Below is a listing of the dungeons;
With the Dungeons being completely different in all the games, the Pokémon found within the dungeons are also different so the Pokémon you will obtain are completely different from game to game. With this, you need to have all three games in order to obtain all 493 Pokémon.
Each game has their own set of Starter Pokémon, all of which cannot be obtained within the other games, in addition to the previous Pokémon. However, if you have all three games, you will have access to all of the Pokémon. Since the Pokémon storage is shared between the three games, you can use any of the Pokémon in any of the games. However, you cannot use Pokémon that are out of storage and in your Adventure Squads in any of the other games. You will have to put them back into storage to utilise them in the other games.
The amount of Pokémon and items that you can store is also dependant on the amount of games you have tied to your save file. The more games you have associated with them, the more Pokémon and items you can store.
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