I like the idea of favoured classes, partly because I use a homebrew campaign setting. I use them as guidelines for what a race's society is going to look like. Elves have more time to invest in study and so there are more elven wizards than say...Elven barbarians. Dwarven society is militant, orcs have a sort of ritualized societal interaction that I think you'd get when most of your race flies off the handle at the start of a fight...That said, I change the favoured classes of races when placing them, because it changes the way they do things. My Centaurs favour scout, not...I think it's Ranger?
Getting rid of multiclassing penalties is a good idea, too. I don't even understand why they're in there except that maybe they thought that, like in 2e, multiclassed characters should just suck more. Instead, every character gains a +2 competence bonus with one skill of their favoured class. If they have a level in that class (people with favoured class Any count their first level as their favoured class), they get a +2 competence bonus to another skill. Tiny benefits, but essentially free, so no one's complained.