Originally for my secret crafts I kept the basic system of circles and percentage chances, and treated them as if they were spell- like abilities. I lowered the xp costs to be more in line with 3e. This seemed to work ok for some of the less combative crafts, such as the Dream Master. But the Dracologist was horribly imbalanced (as they were in the original supplements, as well), and I never should have used the Monster Manual listings for the dragon breath damage...
Now, I'm not sure what I'd do. I originally didn't want to make the crafts prestige classes because it would limit the options the characters had available to them- the Dream Master was also an arcane trickster, and the Dracologist was also a loremaster, and these helped flesh out their characters. There's only so many levels to go around, and in the original campaign I was also limiting people to one prestige class. But it does seem like the sort of thing that should be gotten through class levels, and not through xp spending. I'm not sure what I'd do if I were running it again.
