This answer includes all DLC.
- Weedle line
- Pidgey line
- Rattata line
- Spearow line
- Paras line
- Mew
- Ledyba line
- Unown
- Celebi
- Wurmple line
- Taillow line
- Skitty line
- Spinda
- Castform
- Kecleon
- Clamperl line
- Jirachi
- Deoxys
- Bidoof line
- Burmy line
- Glameow line
- Chatot
- Carnivine
- Phione
- Manaphy
- Darkrai
- Shaymin
- Arceus
- Victini
- Patrat line
- Pansage line
- Pansear line
- Panpour line
- Genesect
- Furfrou
- Diancie
- Hoopa
- Volcanion
- Magearna
- Marshadow
- Zeraora
- Meltan line
- Zarude
- Wyrdeer
- Sneasler
- Enamorus
- Walking Wake
- Iron Leaves
For further help on completing a Living Dex, I would recommend this answer. Though there are some version exclusive Pokemon, it doesn't really matter because you'll need all four games plus their DLC to complete a Living Dex anyways.