I think the way they handled the A/B scenario is fine, and makes a lot of sense. The game is clearly set up to encourage replays, with clear rankings for all 4 scenarios and enabling you to select from any of the 4 scenarios at the menu If the A & B scenarios influenced each other like the zapping system used to do, it would make B scenarios somewhat obnoxious to manage, since you would have to keep saves with the idea A choices on hand or something equally awkward. It also works great for RE.net's weekly challenges; letting you thoughtfully choose which scenario is best for each new task.
In that sense, I prefer to think of the [2nd] scenarios in REmake 2 as a remixed/arranged mode, as opposed to an entirely new scenario. Would it be cool to have 2 different stories? Sure, maybe. But I feel like they got most of the best beats from the original's two campaigns, and let's be honest, Leon A/Claire B in the original was vastly inferior in comparison to Claire A/Leon B.
Though I secretly hope we eventually get a [3rd] super-hard scenario remix at some point down the road.