When working in a way and for a cause aligned with their Motivation, characters should be *better*, They are motivated - propelled by their own convictions and innermost feelings. I'm going to suggest that whenever a character is motivated, the character should have a bonus - another die, for instance. Conversely, whenever they are working in a manner and for a cause opposed to their Motivation, they should have a penalty, maybe one less die.
So Motivations should come in opposed pairs. Some examples might be:
Justice <-> Privilege
Forgiveness <-> Vengeance
Order <-> Chaos
Liberation <-> Oppression
Protection <-> Exploitation
Duty <-> Power
It's obvious that the Motivations on the left would make great Motivations for heroes, and those on the right for villains, but I can see interesting ways these could all be switched.