I have children, we eat a lot of counter service, and I am in favor or this policy - somewhat. I think it needs to be tweaked a little bit. But, I like the general idea.
Back on the seats. Who cares. You are there to eat, not take a nap and relax. It provides a place to eat a quick meal, which is what CS meals are intended to be. If you want to sit and visit for an hour, go to a TS meal. I get the whole idea of having those stools instead of chairs makes for more room. As long as they are sturdy stools, great. If they would have started with stools instead of chairs, no one would have cared.
The whole family waiting in line. This is the part that needs to be fixed. If your kids need to calm down before eating, make them sit on a park bench outside first. But, otherwise, there is no reason that they can't be expected to not sit down until it's time to eat. Do you have your kids come to the table at home and sit down ten minutes before you eat just to calm them down? But, I've stood in the CS lines many times, and they are small and congested. Why not allow only one person and have a spot for other people to stand.
I think the whole idea of the plan is to have people sitting at tables long enough to eat and move on. By trying this idea out, they eliminate the people saving tables, sitting down for a break and just relaxing, taking more time at the tables than the meal takes, and something I've yet to hear mentioned - people who aren't eating food from the restaurant, but instead eating their own that they've brought in.