Yeah, but not all of the victims you save actually acquire Persona's after you face them, not to mention Yu and Adachi obtained Persons without facing their Shadow selves. Likewise Strega, utilized drugs to create the potential phenomena, and even the S.E.E.S. members themselves are all pretty screwed up yet still possess the potential. Part of me was actually thinking about this earlier, as to whether the Investigation Team members actually experienced the Dark Hour or not. It's likely they didn't since Junpei himself only manifested the ability to see the Dark Hour rather recently, whereas the game implies the P3 MC possessed the ability to see the Dark Hour since he was a child.

With all that said, I feel it just shows that having the ability to use a Persona is a special gift that goes beyond one being able to come to terms with themselves. The rules from P3 don't quite add up to P4's rules as characters like Mitsuru already obtain their true ultimate form for their Persona before you can even establish a social link with her. So in truth, the recent series haven't really given a very conclusive formula to determine how one obtains the potential.

As for the gameplay idea, my only issue with it is that it would probably slow the game flow or seriously alter how social links. It would really slow down the beginning of the game. Still, its an interesting idea and I can see how it could work as long as it was designed to have a set story party and then have the alternate Persona characters count as special side characters as opposed to full on party members.