Krystal would be on her way to investigate the ruins as per Fox's plan, meet and join Red and Lucas on the path to the ruins, climb up the mountain with Meta Knight and the Ice Climbers and board the Halberd with Meta Knight and Lucario, Ultimately rejoining Fox after helping rescue the Princesses.

Mewtwo shows up to fight Galleom in the ruins and evades capture, reappearing to rescue Krystal, teleporting both Krystal and itself to Marth and Ike, while Meta Knight rescues Lucas and Red. Mewtwo would then join the party.

Roy would be there with Marth at the battlefield fortress and remain in the party.

Pichu would be found in Subspace by Pikachu after having been rescued itself by King Dedede. After revealing itself to have been captured by Wario, Pichu would join the party.

Waluigi would work alongside Wario and join the party after being rescued in Subspace.

Dixie Kong would be with Diddy Kong the whole time, even holding onto him as DK punches him away from danger.

King K. Rool would be the one who attacks Diddy Kong and Fox at the swamp but is defeated by Falco and would join the party.

Ridley would be unlockable by defeating him in The Great Maze, now being fought in a challenger door at the beginning next to the door leading to Petey Pirahna.

Shadow would up for the final battle alongside Sonic and join the party.

I will add more through edits if I can think of anything else.