Dystopia-fiction, and nothing else.
Maybe not full dystopia, but just enough. The Hero Factory has seemingly made this world a better place, with more heroes than someone can shake a stick at. They're all completely loyal to Makuhero City, but more importantly, loyal to the Factory itself.
I would want to sort of reboot the first year, since it has a great story to build off of. Stormer, Bulk and Stringer are three veterans from the original batch of heroes, and they are ready to retire. Until, they're saddled up to three rookies, being Furno, Breeze and Surge. During this time, various criminals seem to know more than they should; they know when to attack Quaza shipments, know what firepower to pack, and most importantly, know how not to get caught. It seems very strange. Like...there might be a leak, even.
In all of Hero Factory history, there has never been a leak. Every hero is consistently placed under a refreshing 'sleep mode' which seems to wash away most emotions at the end of the day. The Heroes just think it makes them well-rested, but really, it erases individuality makes the heroes servants of the Factory.
One hero has realized this, and is working from the inside to destroy the Factory and save his enslaved brethren; Von Ness.
The story would go that Stormer and his group have to learn that the Factory leadership is manipulating the heroes, but they still have to protect it from falling into Von Ness's hands to protect the civilians of Makuhero. Von Ness and the old leadership are cast out, and Stormer is instated as the new leader of the Factory, making sure that every new hero is allowed to be his own person, without fear of brainwashing or silencing.
That's just my pitch, however. It's rough, but I think it could work. I actually really, really liked Hero Factory and there is so much potential in the theme's story.