There was very little difference. Both ran off of dictatorship. Napoleon did lead with heavy manipulation, while Mr. Jones controlled them by just him having human authority. Both cut back rations often, and over worked the animals with out breaks. But, Napoleon often had animals do his dirty work (such as the dogs being the executioners along with being body guards) while Mr. Jones only made the animals work for him.
In the end, Napoleon equaled no better than Mr. Jones if not maybe even worse.