It would make sense for Phineas to be seen as the antagonist and not the protagonist because of the trouble that he gets in. But it would make more sense that Phineas would be the protagonist and Gene would be the antagonist. Gene is so caught up in his own world and how he feels that he cannot focus on anything except for the jealousy he feels toward Phineas. It is impossible for Gene to be seen as the protagonist when he was the one who bounced the limb and caused Phineas to fall off and break his leg. He could never admi this to himself and eventually Phineas dies in surgery.
Gene is his own worst enemy and has a large load of resentment, jealousy, and fear towards Phineas. He cannot come to terms with it and has to force himselft to take drastic measures. He not only jounces the limb, he plots against him academically, and fails to return Phineas' declaration of friendship on the beach.