After fifteen seasons of riding with me and having employed both techniques, my #1 stoker prefers to step down at stops. I think that sitting still on the saddle at a stop is harder on one's posterior than actual riding. I also believe that stepping down with me helps reinforce my stoker's status as partner/teammate and not just a passenger/power source. Although the rare misses can be embarrassing, it is quite satisfying to nail re-starts with near-simultaneous clip-in. Even better on the triple, when #2 stoker joins the dance. (We will never be one of the the strongest or fastest teams out there, so you'll have to excuse me if I take a bit of pride in captaining one of the more coordinated teams. :-)
Regards,
Dave