A majority of the Legendaries aren't 'God' Pokemon. Most are simply Legendary because they are one-of-a-kind or are protectors of a certain element, or other object.
Legendaries:
Articuno, Zapdos, and Moltres: Elemental Birds; 'Trophies' as said by the antagonist of Pokemon: 2000
Mewtwo: Mew Clone
Mew: Parent to all Pokemon not made by man, or directly related to Arceus.
Lugia: Protector of the Seas
Suicune, Raikou, and Entei: Representations of the North, East, and Western Winds; Reincarnations of three unknown Pokemon
Ho-Oh: Representation of the rainbow
Celebi: Guardian of Time
Regirock, Regice, and Registeel: Man-Made Golems
Latias and Latios: Mirage Dragons; Soul Dew Protectors
Kyogre: Creator of the Seas
Groudon: Creator of Land
Rayquaza: Creator of the Skies
Jirachi: Representation of a Shooting Star; Representation of a Dijinn(Genie)
Deoxys: Pokemon from Outerspace
Uxie, Azelf, and Mesprit: Representations of Knowledge, Willpower, and Emotion; Spawn of Arceus
Dialga: Creator of Time
Palkia: Creator of Space
Giratina: Creator of Dimensions
Manaphy: Child of the Seas; Has power to control Water-Type Pokemon
Phione: Offspring of Manaphy
Heatran: Representation of Volcanos
Darkrai: Representation of Nightmares and Shadows
Cresselia: Representation of the Cresent Moon and Good Dreams
Shaymin: Bringer of Spring; Creates fields of flowers
Regigigas: Representation of Contential Shift
Arceus: Creator of 'Life'.