When Plankton smelled his Plan Z folder, he said that it was 'lemon scented'. This may be just a random joke, until you realize that in "Mermaidman And Barnacleboy V", there's the "Every Villain Is Lemons" joke.
It may come off as puzzling to many at first as to why King Neptune didn't execute Plankton at the end of the film for the crimes that he was planning on executing Mr. Krabs for throughout the film. But when you think it through, it actually shows character growth on King Neptune's part, as he at this point had realized the error of his harsh ways and that Mindy was right, due to the fact that he had gone so far with his obsession with cruel punishments that he was about to kill someone that was innocent. With that combined with SpongeBob's success restoring his faith in sea life, he likely felt that whatever the police were going to do with Plankton was a good enough fate.
Although what that Mr. Krabs said was true about Squidward being more mature than Spongebob, you can see that nobody clapped when Mr. Krabs announced that Squidward was the Krusty Krab 2 manager (and everyone was happy when Spongebob was awarded the manager position at the end). Why? Because any customer who has eaten at the Krusty Krab witnesses how much Spongebob really loves his job and how much he loves satisfying customers. This is as opposed to Squidward who is rude to customers and openly hates his job. It also helps that the crowd at the grand opening is implied to feel sorry for Spongebob when the latter walks away and says "I’m ready...depression." It even helps that Squidward himself wasn’t too thrilled when he got the position and he was more than happy to give his manager pin to Spongebob.
After Spongebob finally develops resentment towards Mr. Krabs who he was deeply loyal to throughout the series, it isn't far off that Spongebob would easily resents Squidward who has done nothing but being a complete asshole to him. However unlike the former, at least Spongebob manages to control his resentment at the end.
There's a few reasons why Mr. Krabs chose Spongebob as manager at the end:
Mr. Krabs's statement about Squidward being loyal and hardworking is proven wrong when through his imprisonment, he experiences the latter caring more about being paid than his own well-being and that Spongebob, someone he viewed as a child, risked his life to save his.
Taking into account his Greed, Krabs hates paying his staff that it's almost his Berserk Button. So, Squidward admitting his want to being paid is enough to make Krabs to change his mind and give the manager position to Spongebob who is always happy to work for him for free. It also doesn't help that Squidward completely fails and doesn't really care in getting the customers to remain loyal to the Krusty Krab, thus losing more money in the process.
Another possibility is that Krabs genuinely did grew a conscience and genuinely felt bad what happened to Plankton if that tear of his is any indication and Krabs wanted to make amends with Spongebob before something like that ever happens again.
SpongeBob using The Power of Rock to free the Bikini Bottomites can seem like a Deus ex Machina on repeat viewings but it actually does make sense with what SpongeBob can usually do and how it ties into his character growth. Throughout the movie, he's been attempting to act more mature and like a grown up, but it's been demonstrated in the series that whenever he's leaning into his natural free-spirit as a happy Manchild, it's when he can most utilize his Toon Force abilities. Thus, his energy guitar solo coming out of nowhere actually does come from somewhere and ties into the movie's message of Be Yourself; he's accepted he completed his quest as the kid everyone says he is, giving him the confidence to fully commit to his identity and utilize the insane, nonsensical abilities that come with it.
A joke is made at the beginning of the movie about Spongebob driving the Patty Wagon, which he HandWaves away by saying: "You don't need a license to drive a sandwich." But of course, it's been shown in several episodes that Spongebob only drives poorly when he gets nervous, and he becomes most nervous when he's sitting behind the wheel of a boatmobile. Since the Patty Wagon isn't a boat, Spongebob is perfectly confident to drive it, and so he has no troubles driving it throughout the movie.
Not only is the Patty Wagon not a boat, it's a giant Krabby Patty. And nobody knows their way around a Krabby Patty like Spongebob.
This makes every single Plankton-trying-to-steal-the-formula plot seem much more high-stakes, as in the end, he doesn't just want to make money off of Krabs's recipe: it's step one in his quest for world domination!
Plankton places a bucket-helmet on King Neptune at the climax of the film in order to control him. Considering the trapdoor that dropped the helmet was already built into the Krusty Krab, Plankton's plan must have had another step to it. Had SpongeBob failed to reach Bikini Bottom in time, Plankton would've dropped the helmet on Neptune after he killed Mr. Krabs. With the god of the seas under his control, Plankton's next step would be to take control of the entire ocean. In other words, Plankton would be in charge of 70% of the Earth.
Imagine how terrible Neptune would feel if Plankton made him succeed in killing his own daughter. And it's implied that Plankton's mind-controlled slaves were aware of their surroundings.
However, since the movie takes place after episodes like "One Coarse Meal" and "Plankton's Regular" where Krabs went too far in getting payback against Plankton, the scene could be interpreted as Krabs finally regretting his past actions against Plankton and feels that their friendship was destroyed forever.
Patrick is attracted to Mindy, but Patrick has always been portrayed an adult, albeit a manchild, while Mindy is explicitly a teenager, with character designer Sherm Cohen confirming she's meant to be 13-14 years old. This would make Patrick a predator.
