Ah, heck, back to the drawing board...
What is it you are trying to accomplish? If you can tell us that, we may be able to help you.
Let's see if I can articulate this... I'm basically trying to enable the learning of monster abilities as spell-like abilities by a class. Now, I won't be using regular spell limitations, but I must put some kind of limitation to stop a character from learning an ability too soon. It won't make much sense without seeing the whole class, but the character will need to pass a Knowledge check (DC 15+X) to identify the ability and a level check (10+Y) to actually learn it. Now, as this must be generalized, I'm trying to decide which statistic to base X and Y on. I think that, as flawed as it is, I'll have to go with CR. I'm trying to assess my options. I'm thinking if I should modify CR in some way, or HD, or anything really. This is still in brainstorm phase, so I'm not set on anything. I just don't want to face the same pitfalls that face the Truenamer.