Thunderscape offers a number of FCB to choose from regardless of race for the setting's new classes. What do you see as some of the biggest potential problems if I were to do the same with all races and classes? That is, allow each player to just choose from a small list of options for their favored class, regardless of race.
In general, most of the best FCB are already on race/class combos that already work fairly well so there aren't big balance issues to making them generally available. Human Sorcerer FCB is a good example of this, since humans already make one of the best (if not the best) race selections for Sorcerers there's really no balance problems with letting anyone have their godly FCB.
I think there are probably some that you would want to restrict for being just a bit too powerful, or particularly emblematic of the race. The Goblin Alchemist bonus for instance.
I do this in my games, one more choice players make when they make a character is which favoured class bonus they want.
In a practical sense it prevents the pigeonholing of particular classes as always of a specific race. I also feel as though some are hilariously bad, so I think it's good to let a player pick a better one.