I can't speak for all system designers at Obsidian, but what I described is my outlook on system design and it always drives the process. Core gameplay prototyping should define the basic style and flow of gameplay, with character advancement being developed from that core.
I think F3's opening did a better job than most at integrating a relatively elaborate CC process into a narrative framework. By comparison, for example, Mass Effect basically just has you build an appearance, select a class and background, and sends you on your way. NWN2 allows you to define a lot of things about your character, but ultimately it's a pretty boring CC experience.
Of those, I think NWN2's CC was the worst overall. You had a ton of fiddly options, but those options were presented poorly; you had no connection to the story; and generally it felt like you were interacting with an interface instead of playing the game. Mass Effect's CC was short and to the point. It was somewhat bland, but at least it explained the basic options clearly, got you into the game quickly, and immediately referenced your background. F3's took a while, but it was well-integrated with the Vault 101 sequence. My biggest issue with F3's CC sequence is that it did not give you an opportunity to use all of your skills in Vault 101. When you finally escape, there are several skills you've had no opportunity to use (e.g. Barter, Big Guns, Explosives, Science [i think] etc.), which makes it difficult to re-evaluate your character before exiting.