Many of the villains in my campaigns are long-term villains that encounter the PCs over and over again and seek to hamper their goals not just in combat, but also out of combat. I would venture a guess that this is the case for many other campaigns too.
Challenge Ratings only capture the challenge posed by a villain in a single encounter and are not suitable for determining the threat of long-term challenges. I propose that Effective Character Level be used for that purpose. Under this system, when the PCs defeat a long-term villain, they get experience as if they defeated a monster with a challenge rating that is equal to the villains ECL. Using ECL for this purpose also enables the DM to check how much of a long-term threat the villain (if well played and considering the PCs to be worth his direct bother) would pose to the PCs. O
Groups of villains can amalgamate their ECL in the same way as Encounter Levels are used to amalgamate the Challenge Ratings of monsters.
I just had an interesting thought. Just as long-term villains are might be better represented by ECL than Challenge Rating, Fighters and other martial classes might be better represented by a Challenge Rating than by ECL if they have no special out-of-combat tricks. This is a converse of the long-term villain situation.