The ship Leo pilots, the Vic Viper, was previously made famous as the ship players piloted in Konami's Lifeforce and the Gradius series.
The chorus to the song that plays during the boss fight against the Vic Viper ("Leo! Leo! Leo, let's go!") is effectively cheering against the player. Leo Steinbuck, the Vic Viper's pilot, was the previous pilot of Jehuty and the hero of the original Zone of the Enders.