The answer lies in the methods of division and control characteristic of any slave society. One might be tempted to ascribe the lack of successful poke-resistance to superior human technology, such as the PokeBall and the Box system. This is the dominant narrative in the popular culture, but most modern historians argue for an alternative analysis, given the ample historical evidence that their servile condition predated the technological advances in slave control made by the Silph Company.

In reality, only social control can subdue such a large population of slaves for such a period of time. Historian Orlando Patterson writes that slavery is a kind of "social death," an alienation of one's humanity—or in this case, pokanity. However, the qualities of this social death are variable, as it is necessary for the owning class to divide the enslaved class against themselves. This can be seen in examples such as the Roman slave society, in which loyal slaves were elevated to overseer positions, slaves which spoke the same language were kept apart, slaves that worked hard were allowed certain rewards, and the possibility of manumission (legal freedom) was held up as an incentive.

The poke question reveals similar methods. It is a well documented fact that slave owners—so-called "trainers"—rarely carried individuals who could talk to each other. The nature of the Pocket-Kantoans aided in this effort, as the vast majority knew little more than a single word, relying on intonation and permutation to convey meaning. The slaves in question were thus unable to communicate with each other beyond simple body language and could not plot large-scale resistance. Those few owners who did keep slaves who could communicate with each other typically did so with races such as Magikarp, which they kept weak and out of their natural environment.

However, simply stopping a mass coordinated effort might not have stopped a wide-scale rebellion if such a thing began with individual slaves lashing out and inspiring others with their actions, if not their words. The masters had to control the minds of their slaves as well. Showing favor to certain slaves, by giving them fruit, candy, or gifts to hold, could keep them willing to obey their masters. The masters' culture encouraged the slaves to take pride in certain skills, in either gladiatorial combat or beauty pageants, which could earn their masters substantial profits. Those gladiators and pleasure slaves which earned their masters money were often given a kind of allowance through a presentation of rewards, as simple as a ribbon or as life-changing as an evolution stone. The most favored slaves often spent more time with their masters than with the least favored slaves, which were either infrequently called out of their cells or even held in a remote location at the master's whim, thus ensuring that those slaves who could most frequently threaten the master's safety were also those slaves least inclined to do so and unable to spend time with those most inclined to do so. Slaves who helped their master capture other, more useful slaves were tempted with manumission—the promise of release. They saw their fellows dutifully help in the capture of others and happily disappear, evidently released. Unfortunately, modern research has uncovered the fact that very few of these were actually freed, most simply being shuttled off into distant virtual prisons against some day when their masters might again need to make quick use of them. Through this deception, the owning class was able to use slave labor to perpetuate the system of slavery itself.

Propaganda played a large role in controlling both the minds of the poke-slaves and in subduing nascent abolitionist tendencies in certain segments of the human population. State- and corporate-sponsored books, television, and film constantly put out stories in which slave owners were heroes, with their slaves as trusty servants who could take pride in their skills and position. Cruel slave owners were depicted as rare and quick to be reprimanded by the kind slave owners. Free pokemon were depicted as savages with no culture or social organization, aside from the occasional criminal gang. They could only receive love and purpose through ownership.

And yet, for all this, there was always resistance. Minor sabotages, allowing potential new slaves to escape, refusals to obey new masters. These and many more were the small avenues of resistance available to a population kept from mass rebellion. But mass rebellion came to Kanto, just as it had to Rome in the time of Spartacus, with the Uprising of Mewtwo. Though he was defeated and viciously slandered and misrepresented in the owning-class press, historians are now uncovering more about this revolutionary figure.

I won't get into how the cycle finally ended, since that's pretty common knowledge.

There have been instances of Pokemon fighting against humans. There was the Great Clone Revolt lead by the Pokemon Mewtwo. Mewtwo attempted to turn on humans after escaping the lab and gathered all the other clones in revolt. Giovanni Industries did a rather large and well-funded coverup, however, so it's not a well-known fact today. There was an excellent documentary called from the 1990's called Mewtwo Strikes Back if you are interested in the details.