I'm thinking archetypes (ex. Brick, Blaster, Mentalist) with a random mutation table for flavor?
Well, DC didn’t really do flawed heroes in its early decades. But a substantial portion of the early Marvel Comics heroes DID have flaws, and that helped with distinguishing them, making them iconic.
For instance, several of Marvel’s Bricks- heroic and villainous- were deformed or monstrous from the human POV. The Hulk, The Thing, The Abomination, Juggernaut and others were all so clearly
other that the writers could draw on Frankenstein and other horror classics to crib notes from. And they were all different enough from each other that each was distinctive.
Marvel’s Blasters sometimes had issues with self control. Mentalists with drawbacks were often idiosyncratic in their flaws.
In HERO, every PC over a certain campaign limit will have disadvantages, and almost all will have hard-coded limitations to their abilities. In other systems, it’s not always as cut & dried.
So for something like this, I’d recommend a cooperative approach to PC creation.
When I ran a HERO supers campaign based largely on the Space:1889 setting, I took a lot of effort clarifying what would or wouldn’t work. A decade later, I tried dusting off that setting for a different group using the M&M rules, and took a more hands-off approach. Unfortunately, that created issues that were detrimental to the campaign’s viability.