If the intention is really to have highly multiclassed characters, I think a system more like d20 Modern (where the base classes are Strong Hero, Fast Hero, Tough Hero, Smart Hero, Wise Hero, and Charismatic Hero, corresponding to the six ability scores). When you have classes like Ranger and Cleric, it seems somewhat counterintuitive to turn around and say "Well, they don't really mean anything. Just pick and choose to get the abilities you want." With the d20 Modern approach, the classes themselves still having mean, while making it completely reasonable to pick-and-choose levels.
For instance, you swashbuckling character is some mix of Fast, Smart, and Charismatic (possibly some Strong). Your average wizard is mostly Smart, with bits of Wise or Fast. A D&D-style fighting cleric is Strong and Wise. A paladin might be Strong, Tough, and Charismatic, etc.
(Note: I'm not necessarily saying I would adopt this system myself. Just that, if we accept free multiclassing as a goal, I think this would be the better solution.)