Nintendo's Timeline of Heroes/What Could Have Been

This is a collection of facts and things that would've come into fruition in the NToH, should it have been completed.

Metroid
Mother Brain would've been the main villain, with Ridley as a side villain. The plotline that he killed Samus' parents would've been canon. It would've had some horror aspects. Takes place on World-1, though this fact remains unknown until the crossover with Mario.

Super Smash Bros.
Bowser and Ganondorf would've been turned into monstrous slaves by Master Hand. At the end, it is revealed that Master Hand was controlled by an unknown entity (Tabuu).

The Legend of Zelda: Majora's Mask
Link would venture into Hyrule's Minus World, Termina. Majora is obviously the main villain, possessing the character Skullie. This would conclude the series of Zelda films starring Link as a child.

Pokémon: Aqua v Magma
AvM would feature Harry somehow transforming back into Pikachu, making him and Tim go to the distant Hoenn region to see how it happened. After investigating a gang war (Team Aqua and Team Magma), they discover it was the result of an alien named Deoxys.

Star Fox
Adapts Star Fox 64. Each character would be motion capture CGI, much like Sonic or Rocket Raccoon. Directed by James Gunn. Takes place on World-2.

Kirby: Star Allies
It is said on the page that Marx was an alternate version of Kirby who was corrupted. This wouldn't be revealed until the last films of the NToH (where Marx would get resurrected), but the one who corrupted him was Dharkon.

Metroid: Acquisition
A sci-fi semi-horror heist film starrting Mario and Samus. Rosalina would have been featured, and played by an Asian actress. Ridley would've likely been the main villain, possible secondary villains included Tatanga and the Shroob Princess.

The Legend of Zelda: Twilight Princess
Unlike the games, the Link shown here is the same one as in previous films. This is the same for subsequent movies.

Super Smash Bros.: The Subspace Emissary
Tabuu would've been the main villain, with a personality similar to Dr. Manhattan and Thanos. The Ancient Minister would've appeared as a side villain, though he would eventually turn against his species' captor Tabuu. Mario would've named him Rob, after the Minister expressed sadness that he wasn't alive, so Mario purposely gave him a human name. Solid Snake, Sonic the Hedgehog (movie version), Mega Man, Ryu and Simon Belmont would've guest starred in TSE during the final battle. The Smash Ball would've been discovered on World-3, said to be able to destroy Tabuu, but a major plotpoint is that no one can seem to destroy it. Tabuu eventually does, and the heroes have to fight him even when he's empowered. When Tabuu is killed, he states that the reason he attempted to turn the multiverse into subspace was to stop two eldritch entities from bringing their war to the multiverse.

Phase 3 and 3.5
There was an idea to split Phase 3 into two parts, with the split occuring after a Smash Bros. film where the team dissolved. Porky may have been the main villain. I think, were I to resurrect NToH, I would've decided against this.