For one thing, the animals did not work as hard or as much under Jones. They had work time and they had down time. They all realize this, but not many discuss it as they are beginning to question what they truly remember since the rules on the barn keep changing. The animals also never went hungry under Jones. Everyone had enough to eat and enough time to recover from the work of the farm. The animals were led to believe (by the pigs) that they were suppressed and treated unfairly which led to the rebellion and the ousting of Jones.
Under Napoleon, the animals are manipulated to work harder for longer hours, and then they are not all equally sharing the benefits. For instance, the cows milk more, but the pigs get the milk. Boxer works harder and longer, and is sent to the glue factory without hesitation. The pigs are no better than Jones...in fact, they are worse since they do not show any remorse or feeling for the treatment of the animals they propose. They reap all the benefits and do none of the work.
The conditions on the farm are far worse under Napoleon than under Mr. Jones and this is shown most clearly through the use of violence. Mr. Jones, for example, commonly used a whip against the animals, as we learn in Chapter One. His farmhands also used a whip on the day of the Rebellion in Chapter Two.
Napoleon, on the other hand, uses deadly violence against the animals. He trains Jessie and Bluebell's puppies as his own personal bodyguards, for instance, and then sets them on Snowball in Chapter Five. He also brutally slaughters some pigs and the rebellious hens in Chapter Seven. Later, in Chapter Nine, he sells Boxer to a glue manufacturer so that he can use the money to buy alcohol.
Napoleon, then, is far more violent and self-interested than Mr. Jones ever was.