The Main Deities
Includes Arceus and the Divines. All temples have shrines to each of them. They are the most commonly worshipped and widely accepted as holy, benevolent beings.
Arceus - the almighty, creator of the universe and the other divines
Mew - the genetic ancestor to all life on the earth
Xerneas - guardian of life and bestower of eternal life
Dialga - guardian of time
Palkia - guardian of space
Kyogre - created the seas
Groudon - created the land
Rayquaza - created the atmosphere
Ho-Oh - guardian of the skies
Lugia - guardian of the seas
Zygarde - protector of the ecosystem
Celebi - Zygarde's aide, protector of the forests
Victini - patron of conquest, domination, victory in battle
Genesect - the patron of necromancy
Jirachi - patron of luck and wishes
Deoxys - represents disease, plagues
Lesser Gods
Other immortal beings that are commonly prayed to for help with their aspect or beseeched to not unleash their aspect.
Azelf, Mesprit, and Uxie - patrons of basic consciousness in every sentient being: willpower, emotion, and knowledge
Regirock, Regice, and Registeel - patrons of the earth (rock and magma, jewels, and precious metals)
Cobalion - patron of light/one-handed weapons
Virizion - patron of archery and other projectile weapons
Terrakion - patron of heavy/two-handed weapons
Keldeo - patron of the art of unarmed combat/martial arts
Articuno - patron of arcane ice destruction magic
Zapdos - patron of arcane electricity destruction magic
Moltres - patron of arcane fire destruction magic
Raikou - god of lightning
Suicune - god of rain and other precipitation
Entei - god of wildfire
Tornadus - god of tornados
Thundurus - god of thunderstorms
Landorus - god of earthquakes
Cresselia and Darkrai - represent the different moon phases, twilight, and dreams and nightmares
Demigods
Few people pray to these, but they are all recognized as immortal beings
Reshiram - embodiment of Yang; represents activeness, the sun, the physical world
Zekrom - embodiment of Yin; represents passiveness, the moon, the netherworld
Kyurem - represents the absence of yin and yang, neutrality
Regigigas - said to have shaped the continents
Mewtwo - the psychic god, manmade
Latias and Latios - Rayquaza's attendants
The Unhallowed
Includes Giratina and his consort, Yveltal
Giratina - the god of antimatter, master over the dead, the guardian to the underworld/Reverse World
Yveltal - the god of destruction, herald of death