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. Veterans 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!
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 seems innocuous at first glance, but when The Reveal happens, that's when it becomes clear the game was warning you. It's subtle Foreshadowing that Bowser is the trueBig Bad.
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 to 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 Britta is involved in Dozing 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 Bowser than the Elite Trio), so this is really Bowser's inner thoughts, despite the fact his dreams are terrifying.
Whenever Luigi gets attacked by a Virus, he takes a lot more damage than Mario does. Mario's had a lot more experience with the Viruses than Luigi does, so Mario must've had an immunity built up.
Why does this game break tradition of having Bowser as the first battle by replacing him with Antasma? Because Bowser was the lesser antagonist and never the final boss in any previous game, now that he is the final boss Antasma has replaced his role.
Why is it that Dreambert, who knows the island like the back of his hand, seemed unfamiliar with Mushrise Park? It's because he knew that place as Mushrise Fields! It was only recently developed into a park by Brickle. Notice when finding the Utilibed manual, he recognizes that name as well as Wake Isle for Wakeport.
Dreambert, who mostly serves as an Exposition Fairy, fights Antasma to a draw. It might seem like an incredibly convenient plot device that came out of nowhere, but remember that Dreambert created the battle ring and was the one who trained the Pi'illos to fight, anticipating impending doom. Also, remember his comments when teaching giant Luigi battle techniques such as that he is "well trained in the art of hammer uppercuts". So it should come as no surprise that he can handle himself in battle.
If you decide to restore your health by using the hotel's services, you'll note that the bros go into the room next to the desk since it's the only free one available. It has a double bed. Not twins; double. Make of that what you will.
Somnom Woods is said by much of the staff to be entirely unexplored virgin forest that hasn't had a lick of human contact in thousands of years, yet not long after going into the forest you meet the Nomnoms. And there's also a lot of boomerang bros, but those Koopa troop members could have been some of the first non-native visitors to the woods since antiquity.
Why do the Pi'illos know so much about modern slang and technology? Look at some of the devices they built, many of which would be extremely high-tech even for this day and age (such as Pi'illodium for example).
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?. Antasma does the same thing to the Dark Stone before the events of the game unfold. It's likely that it was also a living being with a soul of its own.
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...
Even its giant-sized opponents likely didn't fare well, and given that it is prepared with things like armour implies that there were giants that tried to take on Earthwake in the past.
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.
Very few if any, if what the one Zeekeeper mascot in Wakeport said is true. He mentions that most of the island has been developed for tourism but that Somnom woods is nearly virgin old growth forest that hasn't seen a lick of human contact since the Pi'illo times and that would make the unexplored forest mystical and spooky. Of course, it hardly seems like frontier wilderness once you actually play the level, but still it's interesting that it has that kind of reputation.
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?! And that's not even going into what the environmental impact of the incident was. Even the minions think it's scary.
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.
Dreamy Bowser. If he can take over a good portion of the universe without the Dream Stone, how far would he have gone if Mario and Luigi didn't stop him?
The battle with Antasma (not the tutorial one) has one of his abilities be putting Mario to sleep and chasing him through a nightmare, where it's very possible for him to lose a lot of health or even get knocked out. Surely that implies that Mario died in his dreams?! Since when did this become A Nightmare on Elm Street?!