The folks at Game Career Guide have written an editorial/analysis in which they attempt to list some storytelling lessons that they argue can be learned from the title, particularly about player choice and characterization. I personally wouldn't point to Baldur's Gate II as the strongest example of player choice, and I suppose the article contains spoilers on the plot, but after 12 years pretty much every CRPG fan should be familiar with it anyway. Here's a snip:
The single best story element Baldur's Gate II is how the player chooses to react to the fact that their father is a god of murder. Whether the player revels in it or fights against their heritage changes the entire tone of the game. In most games where the player has complete control over the attributes and fighting style of the character, the customization is limited to combat preferences or spell knowledge. In this game, even though the back-story is the same from game to game, the player can shape how their character views the world, and their interactions with others can even change those characters, as well.
One element in the game that could have been removed is the character of Bodhi. Her relationship with the main antagonist, Irenicus, seems a little contrived and redundant. Irenicus is enough of a villain that his relationship with a vampire sister doesn't do much to make him less likeable. If anything, Irenicus seems less evil in his attempts to ascend his sister to godhood beside him. From what the player understands about Irenicus, he is ultimately selfish, so sharing a godhood, even with his sister, seems out of character for him. Bodhi does not have any integral part in the main plot, and may have been a stronger character had she not been a sister to Irenicus. A vampire queen that tries to hunt down the soul of a dead god is more menacing than a vampire queen who is waiting for her brother to do the work for her. Perhaps her relationship with Irenicus was intended to humanize Irenicus, to make the player feel some sympathy for him, but it seems out of sorts to humanize a character who, in all other facets, is shown to be purely evil and selfish.