I am not entirely convinced that Mr. Jones is a good leader or a bad one. I think that he certainly is a flawed leader in not understanding the full implications of his actions. His attitude towards the animals and lack of awareness as to how his actions will be perceived by the animals is what lays the groundwork for the revolution and his eventual overthrow. It is easy to say that Jones is an abusive leader and one who mistreats the animals. However, after seeing what Napoleon does, I am not entirely convinced that Jones is that bad. Jones is a flawed leader because he fails to account that his actions could result in a change in authority structure. He fails to bring more animals into his fold and create some type of wedge or division between them. Jones' actions help to create solidarity amongst the animals. The ones who fail to join the coalition are apathetic. Jones fails to inspire much in way of loyalty from the animals, something that becomes hauntingly compelling in why he is overthrown. At the same time, this is something that Napoleon does not repeat, as he ensures that there is complete loyalty, forced or not, from the animals. In doing so, he demonstrates that he has learned from Jones' mistake in that he will not be overthrown like Jones, even though the ending reveals little difference between him and the humans.
You can compare what Orwell would like you to perceive as Mr. Jones character traits by brushing up on the character from the Russian Revolution he is meant to symbolize.