The Delfino Plaza flooding makes absolutely no sense. Even if all that water was indeed inside Corona Mountain (which already raises several questions, being a volcano and all), once being released, it would have immediately fallen into the sea, thus making it impossible to flood anything. To flood a city surrounded by mountains, in a low area, you only need to pour enough water over it, since the geography will hold the water in place. To flood a whole island, you need to raise the sea level several metres, so it covers the island. And since the sea level is the same everywhere, you need to release enough water to cover the entire world- or else the water will immediately spread through the sea all over the globe, making the rise unnoticeable. Can Corona Mountain hold that much water? Really? And then, after defeating Bowser, the flood disappears in a matter of seconds...
Either the island is much bigger canonically than it is depicted in game which would make it so the flood would take some time to escape the city and go out to sea, or Magic.
Maybe the water is held in place by the ridiculous magical barriers that prevent you from swimming too far away from the island.
So Shine Sprites are the guardians of Isle Delfino's light. If the Pianta are aware of the Shine Sprite's importance to the island, why are they holding contests with the prize being Shine Sprites (a good example being the watermelon-growing contest)? Shouldn't they be more considerate - giving up the Shine Sprite so light can be restored? Shouldn't there be some government officials sent to retrieve them for that matter? Remember, Mario was only tasked with cleaning the island, not retrieving the Shine Sprites.
I have a question about Sirena Beach's hotel. First, why would a 4-star hotel like this have secret passages, like the one that takes you from the men's room to a woman's bathtub? I know it's standard platformer game physics, but what are those passages doing there in the first place?
Maybe all the ghosts made them. At least a few of them, like the Boo painting, are ghost intervention.
What are the purpose of those caged platforms around the pirate ships at Pinna Park? They serve no apparent purpose, visual or mechanical. Why are they there?
Reason: Maintenance. they are there in case workers need to make repairs to the ride.
Why, after being revealed, does Bowser Jr. still use his Shadow Mario disguise at all? I can understand that it'd be a definite spoiler if someone say, got to the levels where FLUDD is stolen or they have to chase Shadow Mario in the 7th episodes of one of the earlier levels before getting the 10 shine sprites required to get to Pinna Park, then yeah he should still wear the disguise as the cutscene hasn't played yet showing who he really is. But why bother after Pinna Park? Mario has been framed as much as he could manage by then, he has been seen by various people being chased by Mario before then in his disguise thus nullifying its use for further framing of Mario. But he still uses the disguise for seemingly no reason. When he is running around with parts for FLUDD he is still disguised. In the chase missions after the reveal he is still in disguise. Even when he is being chased for the Yoshi egg which only happens after clearing the first four missions of the level his disguise is removed in, he is still posing as Shadow Mario. And even for the people who have yet to see Mario chase after him before, during the chases after he tried to get Peach the first time, he doesn't even bother drawing his graffiti M's on the ground when he stops. So what's the point?
Maybe Bowser Jr. just wants to make sure that nobody knows who he is (except Mario, but nobody on the island listens to him anyway), so that people won't notice a pair of Koopas running around the island causing trouble. The residents already have difficulty telling Mario apart from Shadow Mario, but they'd probably notice Jr. in his regular form. If he got caught, he'd call attention to himself and it would put a damper on the vacation his dad planned. I know that Bowser could just do what he wanted anyway, given that he's Bowser, but maybe he was willing to (sorta) play by the rules to have a good time. Aside from kidnapping Peach, all really he does is go hot tubbing in Corona Mountain, so he was probably just personally aiming to kidnap Peach and piss off Mario, while letting Jr. do whatever he saw fit to get in Mario's way as long as he didn't get framed for it (ex. gooping up the island).