First of all, I believe that Lego, or at least Farshtey, intended the universes of Bionicle and Herofactory to connect. I don't know if others have proposed this, but this I believe is the best possible connection, and the one I believe Farshtey intended.
Makuro is one of the great beings.
During the Core wars, he left his planet in search of a renewable source of energized protodermis and a haven from Annona's powers.
He desired to create a robot army that could defeat Annona, as they would be resilient to mind attacks.
He found Quatros, an energized protodermis enriched planet, that's why it falls apart (like Spherus Magna) when the quaza is removed.
He created a society built from robots. His AI system was so advanced, the robots were sentient.
He powered the robots with Energized Protodermis, also known as Quaza.
Eventually, he stumbled upon an ultra-powerful design: Implanting a core of solid quaza into the robots' bodies. At the same time, he noticed that crime among his own robots was growing at an alarming rate.
He created Hero Factory: A police force for his robot universe and a way to test the effectiveness of his new Core-implanted robots in action.
He finally had a design he thought would work: Thresher.
So he told Thresher everything: About the original planet Spherus Magna, the core wars, and his quest to defeat Annona.
Thresher went to fight Annona, Makuro's old nemesis. It was an experiment in mind protection: Robots have no “brains” only computers.
The quaza, or energized protodermis, mutates Aldous Witch when he powers himself with it.
The animals on quatros are obviously rahi.
The doom box was created by four great beings, one of whom is eventually killed.
Black Phantom and Voltix may be Dark Hunters, but this is unknown.
This all works with, and is in fact supported, by the Hero Factory Canon.
What do you think?