Well, in my honest opinion, Team Rocket, as an organization, aren't really all that dominant anymore. They kinda sabotaged it from "Pokemon Emergency" by introducing Jessie, James and Meowth.
On the other hand, even though the executives from HG/SS were there looking for Giovanni, he has not yet disappeared from the Headquarters yet, so what would be their plot? Will they come to say "Agents Jessie and James, you're fired!" or something?