I think WWE have a love/hate relationship with Heyman. With Heyman he has a tendency to go off from the beaten path that McMahon wants.
With the commentary situation you have to look at it from what McMahon and company think about wrestling, and how they ultimately see the product. Yeah guys like Jim Ross and Paul Heyman would be a better team. But a better team from McMahon's perspective is someone who looks aesthetically pleasing on camera. Will be a good puppet. And has the generic commentator look that McMahon goes with(DeGeorge,Mooney,Pettengill,Hodgson(for a brief time),etc.
Just look at ring announcing. Everybody knows The Fink is the best. But b/c of his look, McMahon would rather go with hacks like Justin Roberts.