FREE AGENCY/TRADE ELIGIBILITY
I'm not quite sure of how the logistics would play out, but there could be some sort of trade deadline put in place where Raw and/or Smackdown can make an offer to their rival brand about a certain superstar they might have their eyes on.
For instance, if Shane wanted to make a play to bring Anderson & Gallows to Smackdown, so he could pair the tandem with Styles and put The Club back together, he would go to Stephanie and either offer a certain number of superstars in trade, or possibly ask Steph is there's someone on his roster that she may want to join her roster.
They would then come to an agreement and make the trade happen.
As far as free agency, it could be a situation where a certain NXT star is ready to make his or her main roster debut. Shane and Stephanie would come together and decide which brand that superstar would be a better fit for.
If both want the star, then there would need to be some sort of deal worked out between brands. Maybe one brand offers a star from their roster, in order to claim the rights to the upcoming NXT talent.
Either way, it could be an added exciting element to the whole situation and could be another tool to prevent the company from repeating history.