Smoldergeist makes constant threats about how you'll never make it past the Tutorial Level. One piece of dialogue reveals Peach, who you're chasing after, is easily getting past them too!
The way you initiate the last Giant Luigi boss battle. Usually, Luigi is scared. In the battle versus Giant Bowser, Luigi pulls the cap over his eyes and smirks with confidence. Mario is momentarily surprised by his brother's confidence but they both clasp hands and Dreamy Luigi grows with the words in the background saying things like "Do my best!" and "My big bro!" It's pretty heart-warming too at that point.
Bowser pulling a Hijacked by Ganon moment, usually he is on the receiving end. This time he tricks the villain, instead of the villain tricking him.
It's not just that Bowser managed to usurp power. Rather, it's that it is heavily implied that he was playing Antasma the entire time. He simply pretended to be The Dragon in order to wring all he could out of Antasma, and boot him aside when it was clear there was no more to gain. The key props here is that Bowser was well aware Antasma would perceive his bluster and ego as ignorance. Say what you will about Bowser, he is NOT as idiotic as he appears to be and is still the formidable villain he's always been.
Finishing Bros. It's the move used to end Giant Luigi battles, and it involves Luigi jumping into space and grabbing a star, with Mario jumping on the star and flying it down into the boss's heart.
Star Driver. In the final Giant Luigi battle, Kamek uses his magic to make Giant Bowser grow to truly colossal size. The heroes' answer? Initiate Finishing Bros, with Prince Dreambert using his power to make the star itself grow gigantic, turning the attack into the aforementioned one. Luigi throws the giant star with Mario on it at Bowser, who tries shooting it down with a barrage of fireballs. You have to control Mario and the star by tilting the 3DS to avoid the barrage, finally striking him head on and finishing him off instantly.
The Final Boss. As said above, Bowser betrays Antasma before Antasma has a chance to do the same. Then he takes the Dream Stone, and prepares to wish Mario and Luigi away. Peach and Starlow shatter the stone first... and then Bowser inhales the fragments, doubles in size, starts glowing like he grabbed a Starman, and becomes one of the most awesome final boss battles ever. His transformation looks awesome, the fight is awesome, and you will feel awesome when you win.
The music helps too. Yes, that's right, Bowser gets an incredibly epic, intense and emotional Kingdom Hearts-esque final battle theme that many argue is one of his best yet.
Considering Yoko Shimomura composed the game's music, it's not all that surprising.
The mere fact that Bowser actually manages to remember Luigi's name, implying that Luigi is finally considered a Worthy Opponent in Bowser's eyes.
Bowser: I'LL BE BACK! MARIO! GREEN 'STA— I MEAN, LUIGI!
Giant Luigi vs Giant Bowser. It's easily the best giant boss in the series, made better by the fact you're actually taking down Bowser's dream self, so in other words basically countering his ultimate wish fulfillment. About six or seven phases of attacks, tons of clever ways to counter attacks, a surprise twist finale at the end, great music, and much more make it a fantastic battle, albeit a difficult one.
The final phase has easily the most absurd and actually frightening concept you could think of in a Mario game. See, Bowser can grow giant by himself, thanks to what the Bros. did last game. Kamek used to do that—still can. Even after Bowser is already giant. Three words, people: Giant... Giant... Bowser.
To say nothing of the battle's prelude. While Bowser's giant form startles the Bros. at first, they respond calmly to this threat after numerous other ones and prepare for their final one. While Luigi's giant form had been triggered by a cowering Luigi pulling his hat over his eyes previously, he deliberately sets the transformation off this time. Even Starlow cannot help but note how confident he looks this time around.
A particular moment in the Bonus Boss fight. Bowser Jr starts out the fight in the Koopa Clown Car, but will eventually get out. You can then jump in, and start one of the game's many "chase attack" segments... but this time, the Mario Bros are the ones on the offensive!
He uses the Border Jump minigame from Superstar Saga as an attack. Talk about nostalgia...
A more subtle one: Right before Earthwake attacks, Pi'illoper tells the bros how strong and horrifying it is... and also mentions the word gigantic. During the conversation, Mario looks back at Luigi... who simply nods, realizing what will happen and bravely accepting the challenge.
In the scene right before the final battle, Bowser starts using the Dream Stone and gloats about how he'll destroy the Bros., when Peach and Starlow use Wish Power to just stop him in his tracks and destroy the Dream Stone! Sure, Bowser just swallows the Dream Stone shards, but when you think of it, this means that Peach and Starlow's Wish Power is more powerful than the Dream Stone!
Also doubles as a nice Call Back to the previous game when the two of them also double-teamed him at the beginning of the game to kick him out of Peach's Castle.
And you have to give Antasma this. Bowser's double-crossed him. His plans have been practically flushed down the toilet in one clawing stroke. He could've taken the opportunity to run, but he doesn't. Instead he stands his ground and challenges Dreambert to a duel, the two proving to be equally match. Their fight then moves to the Dream World where Antasma, who's powers are greatly amplified, curb stomps him. When Mario steps in to fight in his place, Antasma buckles down and fights the plumber with everything he has. Yes, he lost like all of Mario's adversaries, but you can't say he didn't go out fighting.
I'm not sure why, but there's something awesome about Prince Dreambert during the battle with Antasma. Sure, he doesn't do anything except heal Mario a small amount every turn, but the look on his face shows that he's done with Antasma's shit and that he's going to support Mario all the way.
Popple, while still a funny and interesting character, Took a Level in Jerkass here. He forbids the bros to pass an area they need to pass since he mistakes a peaceful Wiggler for a security guard, forces them to fight the Wiggler with him, and is not only useless in the Wiggler fight, but a hindrance. And then he betrays them. What follows is probably the second greatest example of Catharsis Factor in the game, as Popple is much easier than the Wiggler.
It gets better. Occasionally you can target Popple before he officially becomes an enemy, in order to stop him from aggravating the Wiggler into using a stronger attack. Cue players unleashing their strongest Bros. Attacks on Popple just to vent their frustration with him.