1) Charisma determines the DC to save against your mysteries. Intelligence determines the highest level mystery you can cast.
2) 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.)
3) 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.
4) 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.
5) 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.
6) You may “swap out” mysteries, just as a sorcerer does spells known. 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.)
7) 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.
