Saying "Ganon's been in more games than Ganondorf" is a really pointless statement, as he was hardly present in any of those games. In TLOZ, he only appears as the Final Boss.
This is especially true in the handheld games, where the real antagonists are simply trying to revive him.
In the Oracle Games, it was Onox/Veran/Twinrova, in Four Swords, it's Vaati, and I don't know about ALBW, but Yuga seems to represent that too.
But in the three games Ganondorf is in, he is the main antagonist. The entire story, he's calling the shots. So naturally, he's way more popular than Ganon.
Besides, Nintendo rarely pulls characters from handheld games anyway. Otherwise, we would definitely have Isaac and Vaati by now.