Given Gen 7’s dark descriptions of Mega Evolution, there is in fact a good chance that Megas will be presented as the new Alphas/Nobles in Z-A.
Megas can be controlled per se by forming a strong bond with a Trainer, but it’s clearly meant to be a hair trigger sort of thing in canon. Even the anime had a similar plot point - Korrina couldn’t control Mega Lucario. Mega Pokemon could very easily go out of control, hence why Mega Energy is only meant to be a temporary power source. The redevelopment of Lumiose City could involve stopping rampaging Mega Pokemon under the command of irresponsible or unprepared Trainers.