Mr. L.'s basic personality traits are sarcasm, greed, jealousy, and cockiness. These traits have appeared before as Luigi's faults... All Mr. L is is the personification of Luigi's personal flaws, the traits that keep Luigi from being too powerful. As a result, he can never win, because he's just an exaggeration of someone's most negative qualities.
The Mushroom Shakes only appear in this game and no other games. Shigeru Miyamoto originally wanted Donkey Kong to be a Popeye Game. Popeye normally powers himself up with cans of spinach. Maybe it's actually a subtle Popeye reference!
The world entrance doors on Flipside Tower are in Roy G. Biv rainbow order: Lineland's door is red, Gloam Valley's door is orange, the Bitlands' door is yellow, Outer Space's door is green, the Land of the Cragnons has a blue door, Sammers' Kingdom's door is indigo, and the Underwhere/Overthere's door is violet/purple.
The Primordial Fruit can be used to make a Town Special dish, and a Whacka Bump can be used to make a Roast Whacka Bump. However, both of these dishes actually heal less HP than their ingredients. This is representative of the Cragnon's wasteful nature, as both those dishes are said to be Cragnon-based.
This is the first game to feature direct combat (ie. jumping on people) rather than turn-based. Why? Because it's the first to take place in a different dimension, that's why.
The title screen. It shows all four of the heroes, but while Mario, Peach and Bowser are taking the front stage, Luigi is seen jumping way in the background. Luigi only joins you in Chapter 7, only to become a part of the True Final Boss in the very next chapter. This makes him more of a Guest-Star Party Member and/or antagonist. Thus it makes sense for him to be in the background, as most supporting characters and villains do.
Guardians of the bridges:
In the very first chapter, you cross two bridges on the way to the final checkpoint. The first is a simple wooden bridge, but the second is much more grandiose and overall better looking. So what's with the big discrepancy in quality? Well, try flipping dimensions around them. The simple bridge is fully functional whether you're in 2D or in 3D, but the pretty bridge is totally flat and can only work for people in 2D.
The fact that each of the two people who run these bridges is an Expy of Mario and Luigi (respectively) makes sense if you consider their characterization in previous Paper Mario games. The Expy of Mario, the always reliable Heroic Mime, runs the simple bridge, and the Expy of Luigi, who is a less successful hero yet a bigger braggart, runs the flashier yet less efficient bridge.
Even more telling is the difference in abilities. Mario is the only character who can flip into 3D, and as such, he would need a bridge that works in both dimensions. Luigi cannot flip into 3D, and as such, has no need for a three-dimensional bridge. In addition, Red is the brother who spent some time in game in the third dimension: he has reason to want to add an extra dimension to his bridge.
The game is called Super Paper Mario. IT'S PAPER MARIO (3D environment, 2D mooks, object, inventory, story oriented) AND SUPER MARIO (2D, real-time fighting, character abilities, levels and goals).
Why do Count Beck and Nastasia recover from their injuries so quickly? Because they're in Dimension D, where they're 256 times more powerful!
Count Bleck/Blumiere claimed to have "searched and searched" through all dimensions while looking for Tippi/Timpani. So why didn't he come across her in Flipside? Merlon says in the beginning that Flipside isn't a world of its own - it's in between dimensions!
When battling Super Dimentio, the use of an Ice Storm attack will yield only the boss' projectiles being targeted. Why is this? Because attack items only target enemies and Super Dimentio is part Luigi!
Note how Count Bleck personally treats his henchpeople. He's giving them their greatest desires. O'Chunks wants glory in battle. Mimi wants to live the fantasies she dreamed up during her likely origin story - being locked away in the dark (the dark becoming her greatest fear) with only her fantasies for company. Dimentio wants... that which Dimentio wants (which even Count Bleck doesn't know). And Nastasia wants to serve Count Bleck in any way she can. And what one of the biggest jobs she does for him? Being directly cruel to people. Count Bleck can't bring himself to do it personally!
Pixls usually have names that indicate their functions. Looking back, the reason Timpani was given the name Tippi by Merlon when she became a Pixl might be because her role in the Light Prognosticus is to give tips to the Hero.
The World of Nothing is creepy enough as it is, with the entire world destroyed (or, more accurately, erased), but then you go to the Underwhere, which is the land of the dead. None of the people from Sammer's kingdom there. Then, a little while later, you find out that the land of the dead is going to be erased too. This is for kids, right?
There's a Whacka in this game, which just so happens to be the last of his kind. You can whack his head to gain bumps, which make for amazing healing items (and an important recipe ingredient). Whack him too many times, you kill him. However, the Flipside Arcade has a lot more Whacka bumps for you to buy. Wait, that one Whacka was the last of his kind. Where did they get the bumps... oh.
At the beginning of the game, Count Bleck sucks Bowser's army into his castle with a black hole. When you reach Castle Bleck, there aren't a huge number of them, but there are a lot of Dry Bones...
Ordinarily, in games like this you save the world before it is destroyed. But in SPM you don't. You get to see all the previous worlds and people you visited whipped out of existence (World 6 actually gets destroyed during your visit, ending after 2 chapters instead of 4, and the second chapter is just a walk through limbo). This game made Luigi an accessory to omnicide.
Maybe even creepier is the fact that Dimentio is shown to be able to simply teleport people to the Underwhere. Even if you're completely, 100% invulnerable, he can still insta-"kill" you.
The game states outright that ALL dimensions are going to be erased without Mario and gang's help. Then they make the implication that the real world also exists as one of the game's many dimensions. So not only does Mario and gang not visit all the worlds that are in danger, everything in the real world could have been temporarily erased from existence without anyone knowing it.
During the final battle, the game briefly cuts to Flopside, Land of the Cragnons, and Yold Town, all of which undergo the same huge tremors and warping Sammer's Kingdom went through just before it was wiped out, but the game cuts away before anything further. When Mario neutralizes The Void, one of the first things seen is Land of the Cragnons getting redrawn. This means that Flopside, Land of the Cragnons, and Yold Town did get erased out of existence briefly. Occasional tremors rock Castle Bleck too, though it isn't certain if Castle Bleck always gets these quakes or if The Void is ready to consume the place too despite being inside of it.
Here's one I just realized. The Castle Bleck main theme? Is it just me or does it sound awfully like the Flipside and Flopside main themes at times?
Despite the Sammer Kingdom being destroyed there is no indication or mention of those who were consumed by the void ever reached the afterlife. Of course it could be Developer's Oversight but the fact that nobody from the Sammer's Kingdom are seen or mentioned in the Underwhere or Overthere (you would think a huge flux of dead people from the same world popping up in the afterlife would be huge) which could mean that if you are consumed by the Void, you are not just dead, you ceased to exist without any kind of afterlife!
Everything about Count Bleck's father and his actions:
Blumiere lived with a strict authoritarian of a father. What else had Blumiere been through before he met Timpani? For how long had Blumiere had to endure?
Doubles as Fridge Brilliance. His actions are pretty bad, but if you remember how important love is both In-Universe and in the narrative, you'll realize that everything he has done amounts to blasphemy. He ruined an innocent love, missed the pain of losing a loved one, and showed his own son a Lack of Empathy for the love between him and Timpani. Even worse is that his tribe was descended from the Tribe of Ancients, meaning that he callously ruined what his ancestors cherished the most; in some region such as East Asia, familial impiety (turning on one's parent/mentor/ancestor/whatever) is a major sin. Long story short, his actions are much more Worse with Context than it may seem. His crimes against love is so severe that his victim, who happened to be descended from the Tribe of Ancients, turned evil and sought to destroy the world.
The story's original driver, the Chaos Heart, makes no real sense. Absolutely nobody would believe that a wedding that took place while Hypnotize the Princess was in effect would be legitimate... except the Chaos Heart does.
When you think about it, a wedding caused by hypnosis and a takeover would be "Chaotic", wouldn't it?