Quoted By:
I don't like Greek mythology, so I'll go with Slavic mythology instead.
Arceus (or Reshiram) - Belobog
MissingNo. (or Zekrom) - Chernabog
Zapdos - Perun
Moltres - Firebird
Ho-oh - Svarog
Lugia - Dodola
Gardevoir - Rusalka
Lilligant - Mavka
Meloetta - Mokosh
Hydreigon - Gorynych
Duscplos - Likho
Salamence- Zmey (Slavic good dragon, often translation of Wyrm here)
Dragonite - Dragon (proper Dragon, Slavic evil dragon)
Lucario - Werewolf (shared by Germanic and Slavic mythologies)
Wooper - Utopiec/Topielec (literally "Drowned")
Quagsire - Vodyanik
Tentaquil - Sea Bishop
Darkrai - Marowit
Forgave me my knowledge of it, for I mostly know monsters rather than gods.
That feel when apart from Jirachi there will most likely be no Slavic Pokémon.