The Alignment system presented in D&D/Pathfinder seems to be one of those elements that people either love or hate. Personally, I like how alignment can act as a useful shorthand in determining a character's moral outlook on life and what they might and might not do. With that being said, I can understand why a lot of people dislike alignment. The system can be rather restricting depending on the character you are trying to play and the system doesn't represent the "shades of gray" morality that a lot of people like to play around with.
Recently, I've been thinking about a few alternatives that one could use in the place of alignment in D&D/Pathfinder, and one specific idea popped into my head while reading through the Mouse Guard rulebook. In Mouse Guard, each character has a "belief" that represents an important idea the character lives their life by. Like aspects in FATE, a good belief is a simple phrase that can both help and hinder the character and should influence how a player roleplays the character. I wonder if you could do something similar for D&D/Pathfinder characters.
Like FATE, every character receives three beliefs that represent the character's core ideas and philosophies. The player of the character creates the beliefs from scratch and the beliefs should affect the character in a positive and negative way during certain roleplaying situations. If you're using action/hero points, you might allow players to spend an action/hero point to gain a temporary bonus in situation where one of their beliefs would help them. Likewise, you can also offer them an action/hero point if they take a temporary penalty in situations where one of their beliefs would hinder them.
If I were to use such a system, I'd probably take Paladins out of the game since I don't feel like re-balancing them to better fit this system and remove the spells and abilities that require the current alignment system. I think this "Three Beliefs" system would allow for more "shades of gray" campaigns and would gives the players a three sentence reminder about how their character thinks and acts. However, this is still just a concept and I'd like to really think this through before I even think about bringing it to the table. However, I'm one of those guys who likes to brainstorm out loud and see what others thing, so feel free to give me your own thoughts and opinions.