[quote=@Keksalot]
>They're only mediocre if you're applying DC/Marvel power levels instead of thinking about how they'd be in the real world. 
It's more "thinking about how characters of DC/Marvel power level would be in real world", really.

>about the characters themselves rather than their powers
Not to say that it's a bad thing but i've always imagined that with superhumans, their powers often define and shape their characters and personalities to a great degree.

>The NPCs are just going to be side characters/villains to help advance the PCs.
In that case could you perhaps help me understand this whole thing better by explaining (if it's not a spoiler) the weaknesses of Jade West, Mannequin, Bison, Toro and Phoenix, the guys who, at least from my point of view, seem to posess powers on a level quite different from the PC's? I think i can guess that Jade's primary weakness is that she refuses to use most of her powers, but that does not really relate to the power itself. 
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But they're NPCs. Their power level is irrelevant. The events in Verthaven were caused by a metahuman of godlike power, are you suggesting that the ultimate threat to human life on earth, a major plot point, should have an equal weakness?

It sounds like you're having a go at the GM for wanting to create a legitimate story, in which characters are frequently outclassed. I'd suggest you think carefully before continuing with the passive aggression.