I don't agree with you, Darklone: The idea of Prestigeclasses is a great one, and it's completely optional, so you can ban them without problem (more so now that many of the old 1-level-classes are worth you while all the way), but to punish people who take them, giving them a big penalty to XP they cannot possibly avoid (except with really rediculous multiclassing) is to harsh, as they would lag behind in levels for quite some time. Better introduce only PrC's that you like (flavour over power) than dishing out harsh penalties.
Getting rid of the multiclass restrictions altogether could be a good thing, but that would rob the humans of another advantage.
Personally, I'll either give each player one additional class they can declare as favored class (humans have two classes which can be about anything) - maybe with the inclusion of Prestigeclasses: you can declare the PrC you're going to take as the free favored class, or any core class.
Also, I'll change the "any" of humans and half-elves in that it means that the class that is most advantageous is the favored class: if they do x10/y1/z1, x will be favored, if they do x5/y5/z1, it's z.
Or, I eradicate multiclassing penalties and give humans something to make up for it. With the new racial weapons familiarity, I plan to give it to every race, anyway. Half-elves and half-orcs either get the human part or the other (not decided yet). Humans can choose any one exotic weapon as their familiar weapon. Alternately, it will be determined by clan/family/whatever. In rokugan, the clans will get something appropriate (the Dragon, for example, will get the Katana, to help them with their Niten Technique), and maybe the ethnic groups of the Realms will get something similar.