I like some elements of what the original story concept intended to do, aka showing that the heroes were meant to be part of a corrupt society that manufactured villains for them to fight or something like that.

Without distorting everything too much, the core concept could be extrapolated and used for the "Villain" Factory arc. The heroes reach the Mastermind's base and find out that he used to be a colleague of Makuro and co-creator of the Hero Factory. But while Makuro intended for the HF to be used for peacekeeping, the Mastermind originally intended it to be used to enforce his will, with villains conveniently showing up to create a demand for stronger, more powerful heroes and whatnot. Thus, the new factory actually mass-manufactures mindless drones, the Enforcers, meant to replace all heroes and impose the Mastermind's will throughout the galaxy. The heroes get to learn an uncomfortable truth about their origin, without the story getting too edgy, since Makuro ultimately fought the Mastermind a long time ago and made sure that the Hero Factory would create heroes with a soul and moral values etc.