These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
YMMV: The Pirates! In an Adventure with Scientists
Crowning Moment of Heartwarming:In chapter three of the book, The Pirate in Green lets the Pirate Captain know that he's planning to get a tattoo of his face with him saying "Scurvy Knaves" on his upper arm and he wants to know if he's OK with it. The Pirate Captain is left speechless.
Pirate Captain: Of course...I...ah...I don't know what to say.
Pirate in Green: Are you okay, Captain?
Pirate Captain: Yes...it's just this, um, ham. It's very spicy and it's making my eyes water.
Designated Hero: Why are we rooting for the pirates again? The only thing they done that's even remotely close to genuine goodness is saving Polly, who the Captain had himself sold. Let's not forget that these people have sworn themselves to looting and gutting people. They are the lesser of two evils in the story and it's a children's tale, but one can still wonder why we are supposed to sympathise with them.
Because they're amusing and it'd be a very boring world if you were only allowed to sympathise with a morally upstanding protagonist.
Designated Villain: Darwin in the first half of the film. Sure, he tried to steal Polly... After the pirates attacked his ship, threatened him with decapitation and tried to murder him for the hell of it.
Draco in Leather Pants: Downplayed. While Darwin isn't much of a villain, the fans still treat him with more sympathy than the movie itself does.
Ending Fatigue: According to the DVD commentary, the film risked this trope during production, since there were so many tiny loose ends to tie up. The Aardman team was anxious to avoid the trope, however, and managed instead to tie up all those loose ends in a Creative Closing Credits sequence.
Genius Bonus: Darwin is cataloging a new species of barnacle when he first appears. Before Origin of Species, Darwin spent much of his career systematizing the taxonomy of barnacles, and was considered one of the world's top experts on such crustaceans.
Ho Yay: There are many moments in this movie between the Pirate Captain and the Pirate with a Scarf that seem to suggest that their relationship may be a bit more than platonic.
The way the Pirate with a Scarf looks at the Pirate Captain when the the Captain takes the wheel just as they are about to dock at Blood Island at the start of the movie
In the Pirate Captain's cabin, there is a figurehead holding a cup with two toothbrushes in it at the entrance to the Captain's bathroom. Obviously one toothbrush belongs to the Pirate Captain, but who do you suppose the second one belongs to?
The scene when the Pirate Captain asks the Pirate with a Scarf to make "nautical noises" to help him go to sleep. According to the director, Peter Lord, Gideon Defoe, the author of the original novels, who also wrote the screenplay for the film, originally wanted to have the two of them in bed together!
Also, during the bathtub chase scene, there are shots where one can be sure that the Pirate Captain and the Pirate with a Scarf are actually holding onto each other!
When the crew leave the Pirate Captain behind after finding out that he had sold Polly to Queen Victoria, the Pirate with a Scarf is the last one to walk away. It is immediately after he does so that the song, "I'm Not Crying" by Flight of the Conchords starts playing. This is appropriate because in the actual clip for the song, the guy starts singing this song immediately after his girlfriend breaks up with him!
After defeating Queen Victoria, the Pirate with a Scarf hands the Pirate Captain his hat back, as a gesture of welcoming him back onto the ship. The Captain immediately responds to this by giving the Pirate with a Scarf a tight hug. The camera immediately cuts to the crew cheering, making it look almost as though the Pirate Captain and the Pirate with a Scarf are getting married.
In the scene during the epilogue when the crew give the Pirate Captain the makeshift "Pirate of the Year" award, the Pirate Captain asks the Pirate with a Scarf if he is a woman disguised as a man. Considering after everything they had been through together, what possible reason could the Captain ask his first mate such a question?
Peter Lord, the director of the movie, stated in the Tumblr page he created for the movie, in his character description for the Pirate with a Scarf, "If the Pirate Captain is the crew's flashy and unreliable dad, then the Pirate with a Scarf is their slightly put upon mum." Pretty self-explanatory, no?
Even in the books, there are some pretty suggestive moments between those two. For example, in the third book, The Pirates! In an Adventure with Communists, when the Pirate Captain offers Karl Marx a cigar, Marx asks the Captain is they had been rolled in the dusky thighs of a native Cuban woman. The Pirate Captain regrettably confesses that they haven't, but then offers to roll them on the thighs of the Pirate with a Scarf, apparently because he's the closest thing they have, despite the fact that they now have Jennifer, a Victorian lady as a member of his crew. Sigh, excuses, excuses, excuses...