Any system that classifies characters into a few categories and presents it as a moral dimension is likely to create problems.
If you want a tool that will help roleplaying, not something to just divide between allies and enemies, it's much better to use a more personalized approach, one that does not attach a value to how the character is described. On the other hand, to be really helpful, the description needs to be much more concrete than the abstract dimensions of classic D&D alignment.
A sample system, one that I'm using, looks like that:
Each character has several Goals, Attachments, Taboos and Ideals (2 to 5 of each seems good). A goal is something the character wants to achieve ("avenge the death of my brother", "find a legendary treasure"). An attachment is a person or group she cares about ("my family", "a priest who saved my life"). A taboo is something she'd rather not do ("I never lie", "I never ignore an opportunity to get rich"). An ideal is an abstract value she follows ("honor", "respect for life"). As a character evolves during a campaign, a player may add, remove or change one of these after each session (drastic events may call for bigger changes).
Just the description may be enough. You may also tie it to the game mechanics. Here are several ideas on how it may be done - choose one or combine several of them.
1. A small bonus to each action that follows a goal, attachment, taboo or ideal; small penalty to each action that goes against them.
2. A significant bonus to saving throws and social rolls if someone tries to force, manipulate or persuade the character to act against his goal, attachment, taboo or ideal (eg. to betray someone he cares about); significant penalty when someone tries to manipulate the character into following one of them (eg. a BBEG asking a character with "never refuse surrender" taboo to spare his life, even as he knows he shouldn't trust the bad guy).
3. Give an action point or similar resource every time a character takes a significant risk or otherwise puts himself at a disadvantage to follow his goal, attachment, taboo or ideal. You may do it like with aspects in Fate: eg. the GM makes an offer "I'll give you an AP if you follow your 'Charity' ideal and help these villagers without demanding payment"
Hope it helps.