Remember what Maynott says to Raoul at one point in the movie? "This is a story about heroes, and heroes don't go to prison." Look at the very last post-credits scene. Hmm, looks like Maynott was right, none of the collective good guys are in that prison cell.
Also, Lucille gave advice that as opposed to Albert finding "someone to give [him] a big break", he should find "new friends". Turns out, in the end, he befriends the pick-pocket in prison and is happier for it.
On one hand, Maynott's dining area is white and pristine. But despite having so many tables and chairs, it's practically empty, save for Lucille and Maynott. This reflects the artificiality of Maynott's popularity, and how he doesn't have friends.
On the other hand, the Rare Bird may be dark whenever Lucille preforms, but it has people there (her audience) who genuinely admire her. And the bright stage also reflects Francoeur's personality, having a pure heart despite his dark appearance.
This brings up Fridge Logic when one wonders why the police handcuff Maynott's hands in front of him instead of the back. Isn't it dangerous not to cuff a criminal's hands behind him? But then you remember, this is in 1910, before certain protocols were invented. The creators of this movie truly did their homework.
Some people are unsatisfied that Lucille confesses her feelings to Raoul, rather than Francoeur. After all, this is a "Beauty and the Beast" story, and Beauty normally falls for the Beast. But it may also be fitting that she falls in love with Raoul, because to fall in love with Francoeur would be loving a flea's shadow. Francoeur may be a sweet and talented and humane, but he's not a real man, so to speak. He's more like a Manchild, hence he and Lucille are Like Brother and Sister. Raoul on the other hand is a real person: he may have flaws and mistakes, but that doesn't stop him from caring about Lucille.
The movie carries a hidden theme that things are not always what they seem.
Emile may seem shy, but he's truly passionate about being a film maker.
His crush on Maud may appear one-sided, but it turns out Maud shares the same feelings for him.
Raoul fights with Lucille but he's truly in love with her.
Lucille is feisty and only pretends to be polite for Maynott, but she shows her true kindness when she meets Francoeur.
Maynott is merely a pompous, vain commissioner who's all talk and no action, but once he meets Francoeur face-to-face, he tries to shoot the poor flea and even goes so far as to nearly shoot Lucille.
A small one, but listen to Maud humming in the opening of the movie. She's humming the lyrics to "La Seine and I" ("I don't know, don't know, So don't ask me why"). How does she know the song if she probably hasn't been to the Rare Bird? Perhaps it's because she's friends with Lucille, just as Emile is friends with Raoul.
Why is it that Pâté makes his HeelFace Turn when Maynott decided to shoot Lucille? Why now, instead of when he endangered the other citizens during the chase, or when he came to realize Francoeur was harmless? Because he too had heard Lucille's beautiful singing. And it horrified him that Maynott would shoot, not just the object of his Villainous Crush, but somebody as talented and sweet as Lucille. For him, hearing Maynott say "Don't.. tempt me" is a big Wham Line.
And more simply, because he witnessed Maynott admitting that he would gladly commit a cold-blooded murder.
On the main page, it's stated that it's a case of Artistic License Law for trying to kill Francoeur (a flea) to count as premeditated murder. And that may be true. However, that's exactly the point. Pate is struggling with whether To Be Lawful or Good, and normally he would go with lawful. But by telling Maynott he's being arrested for essentially trying to murder a Non-human, he's showing Character Development into someone who recognizes the spirit of the law is more important than the letter of the law.
Francoeur's name isn't just meaningful because he's big-hearted. If you look at his face, you can see it's heart-shaped.
When Pâté finds out about how Raoul, Emile, and Charles had a hand in Francoeur's creation, he tries to have them all arrested. Ignoring the fact that one of the accused is a monkey, and my general ignorance of 1920's French law, what could they be charged with?
What would happen if someone swallowed one of the sunflower seeds with the growth formula on it?
Don't fleas drink blood?
Francoeur might've been shot if the growth formula had worn off a few seconds later. The movie was thisclose to a Downer Ending. Think about it.