Pathfinder Bestiary pp313-314 has rules for choosing a monstrous race as a PC class - specifically rules for characters with racial hit dice (as opposed to those defined solely by class level).
In particular, there is a rule for how many levels a CR-based character should advance as the average party level increases: they may start with CR = APL and no class levels, but as the party increases in level, they gain catch-up levels until they are defined more by class than race.
I often use PCGen to add PC-equivalent GM-characters, and use PCGen to boost them from L1 to APL (give or take a level or 2).
If I could use PCGen to generate a monstrous character, say a Minotaur or Ogre, and add the right number of levels to make equivalent to APL, that would be brilliant!
(I can work it out by hand, but the best bit of PCGen is when it works out the number crunching for me...)