Re: Adversarial Answers
Most likely the balance issues, but there are others. For instance, none of my players are proficient enough with the HERO system to build their own characters; giving any of them a Variable Power Pool would be a recipe for disaster as they would have to interrupt me at every twist and turn for me to explain how to build whatever power construct they're attempting.
A lot of it is just personal preference as well. There are a number of 'official' ways to build things that I disagree with and do not use. For example, the Mr. Fantastic wraparound-snare maneuver has been 'officially' printed using Entangle; I don't like this. I just buy it as Extra STR, only to Grab. I also don't use the size/weight templates; if someone is permanently large, small, or heavy, I use Inherent Always On Growth/Shrinking/Density Increase; it makes for a less cluttered character sheet.
To your last question, PCs and NPCs occupy entirely different 'story space' and operate under completely different rules.