As in Tome of Magic, except:
- Charisma determines the DC to save against your mysteries. Intelligence determines the highest level mystery you can cast.
- Grant bonus mysteries per day based on Charisma. These would work just like bonus spells. For instance, if your Cha is 14, you can cast one extra mystery of 1st-level equivalent and one of 2nd-level equivalent per day. (Note that each mystery does give an equivalent level, even though you don't learn them by level.)
- Eliminate the rule that says you have to take mysteries in a given Path in order. If you want to jump around, so as to broaden your versatility, you can.
- Within a category—Apprentice, Initiate, Master—you must have at least two mysteries of any given level before you can take any mysteries of the next higher level. For instance, you must have two 1st-level mysteries before you can take any 2nds, and at least two 2nds before you can take any 3rds.
- Eliminate the rule that says you get a bonus feat equal to half the number of paths you have access to. Instead, you get a bonus feat equal to the total number of Paths you complete. Thus, while you are no longer required to take the entirety of a given Path, there's still encouragement to do so.
- You may “swap out” one mystery per level up as a retraining option (as per Player's Handbook II). If you “un-complete” a Path in this way, however, you lose access to the bonus feat you gained from completing that Path. (You can regain access by re-completing the Path, completing a different Path and choosing that feat as your new bonus, or selecting that feat as a normal feat at your next opportunity.)
- Once your Apprentice Mysteries become supernatural abilities, change the save DC from 10 + equivalent spell level + Cha to 10 + 1/2 caster level + Cha. This makes them useful even against high-HD opponents, and follows the pattern for other supernatural abilities.