I'm not sure about entire games, but I do wish for a few mods for some Elder Scrolls games.

Morrowind: Ability to join the 6th house with an alternate ending where you get to destroy the gods by piloting Akulakhan.

Oblivion: For the Shivering Isles DLC, the option to become Jyggalag (instead of Sheogorath 2.0) and take on all of the island's inhabitants.

Skyrim: Have the Forsaken as a joinable faction for the civil war, become a Briar-Heart, team up with a Hagraven companion NPC.