Abilities scale. 150 potency is 150 potency, whether it's cross-class or not.

What you don't get with cross-class abilities are class traits that improve them (e.g., the trait that takes Stoneskin from 10% to 18% for CNJ) and ability points that boost the power of it (e.g., using Cure on a class that has a low Mind).

So Aero will be roughly as effective for an ACN as it will for a CNJ, since there are no CNJ traits that boost it, and you'll have about the same INT (possibly more, depending on how you allocate your points). Protect gets less effective at level 16, when CNJ gets the Proshell trait to increase magic defense as well, but the Defense portion will still be roughly as effective as it is for a CNJ.