There's always talk that characters need to roleplay, and that characters should be deep, interesting and complex rather than flat, one dimensional or otherwise trite. Indeed any story tends to be better remembered, more appreciated, when the characters, especially the protagonists, are multi-dimensional. And from what I can tell, the complexity of characters is determined by the contradictions in those characters. Woody in Toy Story is friendly and helpful until he's angry and vindictive (for not being the top toy). Ash in Fantastic Mr Fox is at core hopeful and friendly except when he's irritable and insulting (when he feels shown up and not respected). Aang (Avatar: The Last Airbender) is playful and carefree except when he's focused & serious (when dealing with the reality of the war). Or in similar fashion when a character changes from one characterization to the opposite: Han Solo (A New Hope) from selfish to selfless, Mr Fox (Fantastic Mr Fox) from arrogant to humble, Marlin (Finding Nemo) from controlling to trusting.
My problem is in a game like Pathfinder, how can a GM run a game for deep player characters (assuming the players create something of the sort) without heavily tailoring an adventure to the specific characters made for this iteration (if at all)? For example how can an adventure path be written to have a story with compelling protagonists if those protagonists aren't under the author's control? This is especially a concern because of the power granted to the presentation of character nuances by proper setup, good teasing of the potential other sides of characters, which is not possible (or at least far more difficult) when dealing with characters whose actions are uncertain.
So, how does one run complex player characters (and reveal their complex nature convincingly) without effectively custom building an adventure path for those specific characters? Does it matter? Would a more satisfying game be run with stronger presentation of character nuances? I believe so, which is why I want to tackle this.