Remember that the book is about the development of Communism in practice. The farm animals represent the oppressed workers, trying to throw out their rulers (the humans) and set up an equitable society without anybody exploiting the others.
The pigs represent the leadership under the new system. They are, as you say, the most intelligent. But they uses their intelligence to become new exploiters of the rest of the animals. In the end, the confidence placed in them by the other animals leads to a situation in which they are, as observed by the visiting humans, worse off than before. They are exploited more cruelly because the ideology of Animalism simply gives the pigs more excuses to take advantage of them.
The pigs are treated less sympathetically because the pigs become exactly what the humans were: the true enemy of the rest of the animals.
Oh, and the dogs raised and trained by Napoleon are not treated sympathetically, either.