For Heyman's long-term future in the company, I hope not. It's well documented Heyman, Stephanie and Vince don't get along. Heyman is more creative and a better performer on the mic than both collectively. The only reason Heyman is still with WWE is because of how over he is, Lesnar likes him, and together they are doubly over, but that's also because Heyman's role is just to listen to Vince and Stephanie, and it's reduced--he's only around when Lesnar is, which is a few months an year.
Unless Stephanie and Vince have matured, and can work with Heyman in a mature way, making him GM means him having a bigger role in a show, and thus being around more, and thusly, more exposure and opportunities for the three to keep crossing paths, having to interact, and have a falling out.
Besides, I doubt Heyman is interested. Even though Paul Heyman's Smackdown in 2003 is one of the best periods in WWE history, in 2016 Heyman probably isn't too interested, and you can't replicate what he did in his younger days with Lesnar, Angle, Benoit, Los Guerreros, and Mysterio.
I'd much prefer letting Regal try to run SmackDown again as a corrupt GM since his run was cut short in 2008 due to a suspension, but it was so obvious heel GM Regal was going to be epic.
Heyman COULD... run NXT (if he works better with HHH.) That's a limited schedule, and again, he wouldn't have to interact with Stephanie and not as much with Vince who lets HHH run NXT.