Ganondorf/Ganon is not the main antagonist in:
Adventure of Link (He is dead and his minions are trying to revive him)
Minish Cap (Vaati gets a promotion and demoted to secondary player after is is over)
Majora's Mask (Alternate Universe which Ganondorf cannot enter or does not care about)
Correction: He is the main antagonist in the Gameboy Color series Oracle of Ages/Seasons. It requires a code to unlock it though.