You are adept at numerous disciplines.
Prerequisites: Character level 5th, half-elf, multi-talented racial trait.
Benefit: All of your classes are considered favored classes. You gain either +1 hit point or +1 skill point whenever you take a level in any class. Apply these bonuses retroactively for all class levels that have not yet gained one of these bonuses.
Normal: Half-elves with the multi-talented racial trait have two favored classes.
Does this apply to Prestige Classes?
That is one poorly worded feat.
If you were hoping to get more hit points out of your prestige class you could take toughness instead, which would give you an extra HP for ALL your levels, not just the PRC ones.
So as a GM I'd probably allow it. For PFS though the answer would be no.
It is not even worth a feat. Maybe it could be a trait.
Of course you would gain the benefits of favored class for your prestige classes. Note how the feat states that you gain the bonus for any class. The point about not being able to take a prestige class as a favored class becomes completely irrelevant.
After all, the standard convention for rules contradictions is that specific overrules general. In this context the Feat is far more specific in what it does than the blanket statement that you cannot select a prestige class as a favored class.