Magical Animals and Mental Characteristics
Let me provide more of my thoughts on this subject. RoP:M states that intelligence is a free choice for magical animals. To me, that means that magical animals can have a base Int varying from -3 to +3 (barring exceptional virtues/flaws), just like any other intelligent creature. There is no indication that the "standard" Int for a magical animal is -3. In fact, such an assertion is not in keeping with what is shown in RoP:M for beasts of virtue and other magical animals. Yes, regular, mundane animals that are elevated to become familiars move from having Cun to having Int -3. But that's the case only for the specific situation of a regular, mundane animal being made into a familiar. Magical animals are different. Some of them are intelligent (i.e., have Int instead of Cun) long before they ever get made into a familiar. As such, a rule that applies to mundane animals being made into familiars does not apply to them. For example, if I seek out a Raven of Virtue for my familiar, I will find that the "average" specimen has an Int of +1, and had that Int long before I ever meet it. To suddenly say that the smartest Raven of Virtue out there is Int 0 runs counter to what is set forth in RoP:M.
You state that "[f]or creatures with cunning instead of Int this means -3 Int is considered the base of the typical creature." I agree with this. However, I disagree that all magical animals start with cunning. As noted above, some magical animals begin with Intelligence (it is, in fact, a free choice for magical animals). Therefore, any magical animal that chooses to have Int should be assumed to have a "base" Int of 0.
Per is easy, I don't think any of us deny that Per can be positive for an animal, magical or mundale. There are just too many examples given of animals with positive Per.
Com and Pre are more difficult, I admit. But I'm persuaded by silveroak's observation that once you've given an animal the ability to speak (as many magical animals do), much of the reason for keeping Com and Pre low ought to disappear. I further note that the examples of magical animals given in RoP:M do not follow your proposal. I note that of the magical animals specifically disclosed, their Com varies from -3 to +1 and the Pre varies from -3 to +2. (FWIW, the lowest of these values are for animals who cannot talk.) If we include dragons as magical animals then it all goes out the window, as dragons are shown as having potentially very large Pre and Com (and Int for that matter).
So, I guess my point is that magical animals and mundane animals have very different mental characteristics. We should not limit the characteristics of the former based on the characteristics of the latter.
Also, I assume that you propose the same limits for humans and ghosts that you propose for magical animals, i.e., that they must be within +/-3 of the base value (0) for any characteristic. So, your proposal would not allow the Extraordinary [Characteristic] virtue or the Weak [Characteristic] flaw for any such familiar.