This is a preference thing. If you have to make changes to all of them, you would be better of having Choice Plus with a multi-city. If you think you may need to drop a leg or adjust one, do it as multi-city.

I was looking for the note, but maybe JDiver or BRP will know it, but I believe if you have reservations on AA or AA to oneworld, you will ALWAYS be protected with AA, no matter if they are in the same PNR or not.

The old "needs to be in the same PNR for protection" argument is mainly for connections involving multiple airlines and show up via interline agreements. Please correct me if I'm wrong, but I'm like 99% sure of this.