The development of these two games is a rather interesting and complex one. There were going to be three games, collectively called "The Triforce Series," and would link to each other to form a complete narrative. The "Power" chapter would have gameplay focused on changing seasons using the Rod of Seasons, the "Wisdom" chapter would focus on puzzles involving color and a Magic Paintbrush item, and the "Courage" chapter would focus on time with the day changing between morning, noon, afternoon, and night. However, it was soon agreed that linking three games together in one continuous narrative, but allowing the games to be played in any order, would be too complex (indeed, you would be able to play through such a combination six different ways). Thus plans were changed to just two games, with story and gameplay recycled into the games that became Oracle of Seasons and Oracle of Ages. As The Artifact entry on the main page explains, elements of the original trilogy intent remain in the final product when one knows them to recognize them.
In addition to the above plan, one of the games was going to be a remake of the original NES Legend of Zelda.
Hyrule Historia reveals concept artwork for Ganondorf, who only appears as a mindless Ganon, meaning he was considered but cut for unknown reasons.
The Oracle of Ages/Oracle of Seasons have the same names as 2 of the goddesses that created the Triforce, Din (the Oracle of Seasons) is the Goddess of Power. Nayru (the Oracle of Ages) is the Goddess of Wisdom. And Farore, the Goddess of Courage, appears in the linked version of the two games (where you link the two together to get the true ending). It's never made clear whether this is just a case of Name's the Same or if these are the goddesses who created the Triforce.