Vecna is the main antagonist, as he is in greater opposition to our protagionists.
The Mind Flayer is the broad, all consuming Celesitial ruler of an entire dimension (maybe the supreme being of multiple), Vecna is simply the commander of a fraction of his Earthly forces. The Mind Flayer simply seeks to expand his Empire. He is, by nature, incomprehensible in every regard, meaning he can't serve as a true antagonist. Vecna is understandable, as he is human, like the viewers. The Mindflayer's goals are impossible for any human to summarize or comprehend, but the basic understanding of them suggests he desires uttermost power over life, putting him at too broad a motive against our heroes. Vecna has the more knowing motives, thus we and the protags can greater counter him.