Click here for Wild Mass Guessing for the series as a whole.
Bowser was Obfuscating Stupidity the entire time.Bowser wasn't suffering from Amnesia at all. He knew full well he inhaled and swallowed up everyone. He was pissed. It was Disproportionate Retribution for everyone continually thwarting and defying him. The Mushroom Kingdom is his, which includes its inhabitants. When the means to punish them for kicking him out presents itself via Fawful, he rampages right back there. With them in his possession, Bowser had no intentions of interacting with the Marios, lest they escape and start screwing up his plans again. Leaving them to the mercy of his body. When Fawful initiates the next stage in his scheme to revive the Dark Star, he abducts Peach from the Koopa King's fat gut, he rages "Put her back!", revealing he knows what he's doing. This makes their escape in the ending all the funnier, Bowser claims he's disgusted the Marios (he didn't care about the Toads) were inside him the whole time, unwilling to admit it was his own deliberate intention all along.
This iteration of the Mushroom Kingdom was the world "rebuilt" in MOTHER 3.Midbus's pigmask insignia serves to suggest he is a Chimera
The final battle took place in Bowser's heartIt's a very minor note and there's no evidence to say so, but it does make sense considering the theme of the game.
The broken red pipe led to Plack Beach or Bumpsy Plains.It seems logical because those are the only major areas that don't have a pipe leading to them in-game and there aren't many other places for the pipe to go. The only question is where the other red pipe is.
One of the pipes leading to Blubble Lake was originally going to go to Plack Beach or Bumpsy Plains.But it was changed at some point in development, likely because of how large Blubble Lake is and how small the other two areas are by comparison.
The Junker boss is a prototype that was in the trash because of how glitchy it wasThe Junker robot is an early model of a robot (Likely a Jailgoon, Mechawful, or a Dark Mechawful), or a new robot that was cancelled altogether, that was discarded because of how uncontrollable it is and/or because newer versions were developed, but Midbus liked it and gave it a trash can as armor because it was thrown away before it could get real armor. The Junker Cans are just regular trash cans, but are controlled by the enemies inside it. The Junker Cans that don't have any enemies in them are actual robots that were confused with trash cans, hence the garbage inside them, or they were given trash to make them more like real garbage cans. It's also possible that the Junker Cans were part of some automated trash disposal service and were in the trash either dropping off garbage or because they were thrown away.
At the end of the game, Fawful didn't dieWe already know that he has access to soul-containing technology from the first game; what if he designed a device to collect his soul should he die? Then, in Mario & Luigi: Partners in Time, we see Fawful collecting beans for some unknown purpose. What if he used those beans to create a backup body for himself? Given the wackiness of the Marioverse, it's not that unlikely that Beanish folk are actually made of beans. Though he's an Engrish spouting goofball, he's also smart and dangerous enough to conquer the Peach's and Bowser's castles by himself and almost bring about The End of the World as We Know It. Surely Fawful is smart enough to have some sort of backup plan. So, when he exploded, his hypothetical device would hypothetically attract his soul like a magnet and then put it in his hypothetical artificial bean body! It makes perfect sense, kinda!
The Dark Star is an artifact of the Ancients in the Kirby franchiseConsidering an image of it appears on the Lor Starcutter's sail during the fight with it and Magolor in Kirby's Return to Dream Land and that it carries the star motif (albeit in the Mario style) and is so hugely powerful like so many other Ancients-linked artifacts, it seems plausible the Dark Star originally crash-landed in the Mushroom Kingdom from Kirby territory.