As with every game, Pokémon Mystery Dungeon Time & Darkness have a variety of Pokémon exclusive to the games. These Pokémon are fully obtainable through sending missions between the games which result in the Pokémon being obtained. However, this excludes Mewtwo & Celebi which are completely exclusive to their games

Exclusive to Darkness

Pic: Name: Type 1 Type 2
Mewtwo Psychic na
Burmy
Wormadam & Mothim are found in Time
Bug na
Buneary Normal na
Lopunny Normal na
Rotom Electric Ghost

Exclusive to Time

Pic: Name: Type 1 Type 2
Celebi Grass Psychic
Combee
Vespiquen is found in Darkness
Bug Flying
Pachirisu Electric na
Riolu Fighting na
Lucario Fighting Steel

Only Obtained in Dungeons Unlocked By Events

Pic: Name: Type 1 Type 2
Ekans Poison na
Arbok Poison na
Diglett Ground na
Dugtrio Ground na
Gastly Ghost Poison
Haunter Ghost Poison
Gengar Ghost Poison
Ditto Normal na
Articuno Ice Flying
Mew Psychic na
Treecko
Only if not chosen as Starter or Partner
Grass na
Grovyle
Only if not chosen as Starter or Partner
Grass na
Sceptile
Only if not chosen as Starter or Partner
Grass na
Kyogre Water Na
Groudon Ground Na
Rayquaza Dragon Flying
Heatran Fire Steel
Giratina Ghost Dragon

 
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