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.
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 Miyamato 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' Kingom'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 guess which hero you DON'T have in your party for the final boss. You know, the guy who appears in Chapter 4 as a boss, then again in 6, and finally joins you in Chapter 7, of all places, only to be combined into the final boss due to his hidden, supposedly "dark" powers? Yeah, it's Luigi.
Guardians of the bridges:
In the very first chapter, you cross two bridges on the way to the final check point. 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, realtime 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!
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 Pixls are hilarious Cloudcuckoolanders, until you realise that they have been locked up in chests for thousands of years and the isolation has probably driven them insane.
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?