I liked the intent behind the 3e implementation of favored classes, it wasn't so much 'All X are Y', as much as 'Any X can dabble in Y'. The only problem really popped up where the new classes outstripped the races.
The thing with multiclassing was, I'm pretty sure it was intended to limit too much dipping of the kind that a lot of builds take for granted. The classes weren't originally built for that kind of play. (frontloaded paladins, 2-level fighter dips, a barb dip for pounce, etc) Of course, then some folks just do the same thing with PrCs...
I liked the intent behind PF's multiclassing, but yeah, the alternate options got out of hand.
There should be a solution for that kind of free, dip-based multiclassing, but I think it needs a different class structure, without frontloading of numbers and class features. (I take out penalties for multiclassing in mine, but then I also restructured save and attack bonuses to be simpler. Instead of two save tracks, I use one save track, and a single, non-repeatable (and starter-only) feat that builds in the +2 start and a scaling increase. If you multiclass and already have that starter feat, you get a bonus feat for some other use, but you don't drastically over-stack the save bonuses, keeping them more in-scale. Attack bonuses are divided into two camps, full and half.)