All the origin/companion stories are, are side quests.

The main quest (the game) happens regardless of what character you choose to play or group with.

In the older BG games, you had templates with stats/names/and if I remember a generic story assigned in the those are basically origin stories...except in those games they did not tie in side quests based on the characters...if anything the older bg games were lacking in diversity and uniqueness of the main character even more so than EVERY character you made was the adopted ward of some great wizard who gets thrown into the mix and is someone special....

At least now you are some random person thrown into the mix because you are someone special (custom made) and/or you are also some warlock who lost your village as a boy and made a devil's pact you regret, a mage who holds the end of the world in his life/death, a cleric who was spurned by one god and brooding with the opposing god, a vampire minion who is abused and spiteful and wants to free himself, a failed warrior from another plane who struggles with proving herself and being one with her people again or becoming a lone wolf and joining the rest of the as you do the main quest you also learn about the lore of the game unique to that character...which is supposed to create replayability, but that is subjective to each player.