Unmarked spoilers below!
Bowser and the Koopas' Staff
- Bowser no longer being driven with power and learning to treat his minions better.
Bowser Needs Minions!
- When being chased away by Bowser, Wario and Waluigi try to jump through the staircase's bars. Waluigi easily slips through, but Wario's weight gets him stuck. When Bowser makes it clearer what he wants from them, Wario manages to get the attention of Waluigi, who was still within earshot of him. This implies that Waluigi waited for Wario to escape as opposed to just going down the stairs without him.
- Mario and Luigi's high five when they recover their first star.
- Peach and Goomfrey's secret friendship for most of the former's kidnapping.
- All of the Whackas are extinct as of the end of Mario's Quest, but the last one dies saving Peach and Goomfrey from a Boomerang Bro.. He also is reunited with his parents in The Overthere.
- Unlike Mario's Quest, most of the "bosses" that the heroes face are either Anti Villains or genuinely nice. Case in point: Blooper was willing to trade his Energy Cell for his missing tooth, and Lady Bow gladly rewards the heroes her Energy Cell to reward them for exposing the impostor posing as Bootler. As for Francis, when Luigi and Captain Toad realize they went too far in destroying Francis' picture of Lady Bow, they made it up to him by giving him a date with Birdo.
Francis: *sniffle* You guys are the best.
- They also replaced the picture they destroyed in the finale.
- How does Luigi manage to un-hypnotize Peach? By triggering a series of flashbacks in her head of all the happy interactions she had with Mario in some of Goomzilla's previous videos, simply by screaming Mario's name. Whether he did this intentionally or he was just despairing that he may never see his brother again is up to debate, though.
- When Luigi finally frees Mario, they share a hug (pictured above).
- As if Koopa willfully working with Luigi to stop Solus wasn't enough, he also gives Yoshi his power back.
- Bowser no longer being driven with power and learning to treat his minions better...again.
Yoshi and the Lost Egg
- Receiving the best ending (and some of the more positive endings that aren't the best one) has Birdo be reunited with her baby, and Yoshi recovering the eponymous lost egg.
- One of the more bittersweet endings has the Village Leader gently comforting Blue Yoshi when the egg wasn't found.
Mario's Unexpected Transformation
- Despite Mario's fears that Peach won't love him anymore now that he's a Goomba, he still goes to save her. But Peach knows it's Mario the moment he finds her, putting his fears to rest. And it gets even better from there.
- Peach laying out fresh fruit for a weak Kamek, who had to eat nothing but Goomba food for a presumably long time.Kamek: Ah, thanks, you're a star!
- Even as the main antagonists, the Duplighosts compliment each other on their disguises like true friends. Doopliss was also apparently a good father figure to the captain of the Great Glory.