In Bowser's Dream, when he jumps into the abyss in a rage, a Paratroopa specifically states that a fall from that height would be fatal. Surely, he's just concerned for his boss, right? Wrong. In the previous game, something happened at times when Bowser's life was in peril. The game is warning you. Newcomers to the series are scratching their heads at the suddeness of it all. Veterens are having an Oh Crap moment and fumbling for their styluses.
In Dozing Sands, Mario and Luigi relearn the Mini and Mole Mario moves. The character who teaches them this mentions that he saw it in a movie. Well, at the end of Superstar Saga, it is revealed that Mario and Luigi's adventure has been turned into a film at the Yoshi Theatre. Were the moves learned from that movie?!
While you're rescuing Bedsmith, Dreambert appears in the dream world with you in his full body form, instead of the pillow-head form he usually takes when you're in the dream world. I thought this was just a mistake, but then, when you fight the giant boss, you see there's even a 3D model for full-bodied Dreambert. I couldn't figure out what was different, then it hit me in the last world. Most of the time you use Dreambert in his pillow mode to enter dreampoints. This time, however, you're using the petrified Bedsmith. Dreambert went through the portal with you, and that's why he's in his real-world form! The Dev Team Thinks of Everything!
You notice how that despite Bowser and Antasma each having their own unique Leitmotifs, whenever the two show up, only Bowser's Leitmotif plays? It's subtle Foreshadowing that Bowser is the trueBig Bad.
Antasma barely seems villainous in any of his appearances, and even his death seems a bit anti-climactic—at first. Then you step back to look at his character arc as a whole, and you realize he's meant to be a Tragic Villain. The particular way Dreambert pleads with him in Dream's Deep, the fact that the Zeekeeper considers him no more than a nuisance, the whole From Nobody to Nightmare motif, his constant flip-flopping in the face of world domination being practically handed to him courtesy of the Dream Stone... and what does he ultimately wish for when finally given the chance? Merely to be able to travel freely between the dream and waking worlds. NOT world domination, as you would expect. All that combined with Bowser's betrayal being played for tragedy is enough to qualify the whole situation as a Tear Jerker. All he really wanted was to spread his wings—to live a little—and you had to go and kill him...
For a while, you might wonder why Peach is at Neo Bowser Castle and when the villains managed to capture her. Then you realise that the game never actually shows Bowser's wish on the Dream Stone, and realise that said wish must logically have been have Princess Peach with him.
One must wonder why Broque Monsieur is in Bowser's dreams, despite not being involved in Neo Bowser Castle (i.e. how Brittle is involved in Drifting Sands, so there's a Dreamy version of her managing the shop). Well it's simple ... Broque Monsieur was one of Bowser's closest allies in the last game (he was more loyal to them than the Elite Trio), so this is really Bowser's inner thoughts, despite the fact his dreams are terrifying.
After a certain point in the game, you have the opportunity to fight Gold Beanies that drop some very nice rewards. However, they are only found in the Dream World and apparently do not exist outside of it. So what about those Gold Beanies from Superstar Saga?
After Superstar Saga, the Gold Beanies went extinct. The ones you see in the Dream World are the imaginations of the normal Beanies.
Perhaps it could be that Beanies are only native to Beanbean Kingdom and that a Beanish immigrant imagined Gold Beanies while they were bored one day.
The gravity-based Luiginary Work you use is controlled by spinning around the platform Luigi's sleeping on. The only problem is, how is Luigi's body and subconscious supposed to know what direction you've spun the platform? The platform's as level as it will get because it's floating on the water, and it could be possible Luigi doesn't sleep on it perfectly aligned. It might have something to do with the fact that it's a Dreampoint.
Because of Antasma's actions in breaking the Dark Stone, all of the Pi'illos had been petrified rendering them as immobile pillows. So one has to ask: if it wasn't for Luigi's ability to open up dream portals, would they have stayed like this forever? One of the rescued Pi'illos seems to imply this at any rate, "If you hadn't come..."
At the end of the game, the Zeekeeper destroys the Dream Stone... which was a living thing. Remember talking to it in the dream world?
On the other hand, it was also kind of a douchebag, and attempted to kill you for bothering it. So no great loss.
Makes you wonder what happened to the Dark Stone's Spirit, presuming that it had one. Did that split up as the Dark Stone did? Might have been a nice chap.
At one point before the Earthwake battle, the Pi'illo collector guy talks about how a 'terrible guardian attacks anyone who tries to claim the Nightmare Chunk', and then talks of the countless others who've tried and failed to get it. And that it's wrath was severe and horrible. Now keep in mind that this boss you fight is... pretty much a Humongous Mecha that the bros can only defeat thanks to a giant Luigi. What the hell happened to the last people who tried it, the ones who couldn't become a few hundred feet tall? It makes you wonder how badly mauled anyone ended up after trying to take on That One Boss with a few hundred times size different between them...
Similarly, the game outright states that Pi'illodium has been guarding the Pi'illo Temple since the original kingdom collapsed and all but implies it's killed a heck of a lot of intruders since then. I mean, it even says something like 'cue mercy plea' at one point in the battle. And considers missiles, lasers and explosives as a 'reasonable' way to take out intruders. You just have to wonder how many previous adventurers/parties got blown up trying to go anywhere near the centre of Somnom Woods.
After summoning Neo Bowser Castle, Antasma and Bowser test it out by firing on nearby islands. If the islands were inhabited, how many people were killed?!
The game actually comments about how many rare species were made extinct by the castle's disintegration beam due to the island exploding, so you also get the horror of imagining just what the environmental impact of the same was.
Even though it was Played for Laughs, Private Goomp talks about how he wants to "boss around Kamek" and eventually Bowser. Well it isn't the first time they haven't bossed around Bowser before. Their thoughts of eventually betraying Bowser are still there.
Also, Kamek seems to boss them around. It could also be to prevent another betrayal like last time, as Kamek (Or a similar Magikoopa) calls them "mutineers", until Bowser allows the three to stay with the Koopa Troop.