There are really two justifiable answers to your question, though I believe that there is one best answer.
Snowball was a brilliant pig. He made the plans for the windmill. He adapted the commandments, but Napoleon took everything Snowball did and manipulated it to his own purposes. Napoleon was the smartest pig on Animal Farm because he defeated and outmaneuvered Snowball.
Snowball wasn't "smart" enough to see how Napoleon was out-strategizing him. Napoleon saw well ahead of time that Snowball would be a hindrance to his own consolidation of power, so he prepared by taking Jessie's puppies. He trained them quietly and in private and eventually used them to drive Snowball from the farm.
All of these maneuvers are a representation of (or allegory for) individuals from the Russian Revolution. Though Leonid Trotsky was a brilliant thinker, he was out-strategized by Stalin. Stalin used his position as General Secretary to appoint friendly (or pro-Stalin) individuals to government posts. Trotsky was eventually expelled from the party and the country. He was finally assassinated while living in Mexico.