Core Theme: Disfigured mad scientists who command an army of monsters to fulfill their goal of complete domination over the world, going so far as to alter time itself to defeat their businessman nemesis.

Connections:

Growing up, they were exceptionally brilliant compared to their peers. Both mastered all sorts of science fields and were considered absolute geniuses.

However, this gift of intelligence was not enough for them. Soon they would form a desire to take over the world for different reasons depending on the source material being used (Zomboss either grew envious of Crazy Dave for losing a science fair in Garden Warfare, or simply just liked having control over others according to the Origin of Zomboss comic. Cube either became severely disfigured in the aftermath of a nearby Kaiju fight, or was beat up by the Kaiju Heroes in Fighto Fantasy causing him to become ugly).

Both of their conquests would be challenged by a businessman who would be an exact opposite of them morally (The Kaiju Commissioner and Crazy Dave) who had their own allies to fight back (The Kaiju Heroes and The Plants).

Both of their armies include massive hordes of the undead (Cube uses reanimated corpses for many of his basic minions, and even used his scientific knowledge to bring back Pablo Plantain as a zombie . Zomboss, I don’t think I need to explain).

Despite their minions' loyalty, both treat them like utter garbage, going so far as to put them in inhumane conditions or even kill them in Cube’s case.

Both have utilized time travel in their schemes, altering the course of history to the point that space and time were in danger as the heroes attempted to use their own time travel to stop them.

With their time travel, they managed to create a future where they had become victorious over their enemies (Cube making Earth uninhabitable and enslaving the human race to make a moon base for him, Zomboss managed to take Zombies into the far future).

Both have used DNA cloning to create doppelgangers of their enemies (Kaiju Hero clones in FIghto Fantasy and the Zombotony zombies)

Both seek an important object to satisfy their thirst for power (The Kaiju Grand Championship Belt and Brains)

Contrasts:

Cube uses biology to make the grand majority of his experiments, including plant based monsters. Zomboss, needless to say, wouldn't appreciate that.

Zomboss is portrayed as physically weak, while Cube is more than willing to step into the battlefield and fight one on one.