It was a good idea for the magical woman to give Mother a fairy daughter, rather than a human one. With the fairy's growing up so fast, Mother was able to raise Thumbelina, watch her get married, and presumably give her tiny grandchildren. Had Thumbelina been a human living a normal life span, Mother would probably have died of old age before her child was fully grown.
That might have less to do with her being a fairy and more to do with her being born from a flower...
Continuing that idea; tiny semi-adult? Inconvient, but still easy to take care of. Tiny baby? Accident waiting to happen.
Initially, the 'story' about the sun that Thumbelina tells to Mr. Mole sounds like it merely projects her childlike belief that Winter has wiped out the world as she knew it. But looking back, it's also a song meant to mourn for Cornelius, and how he was claimed by the cold trying to find her ("Winter has killed everything, even the sun".)
The climax during the wedding becomes Fridge-Awesome when one realizes it ties in with how she wished she was big. But once she decides what her heart wants, this is the moment where she puts her foot down and stands up to everybody, even though they are all bigger and/or taller than her.
In the opening scene, Jacquimo cites "Samson and Delilah" and Romeo and Juliet as great, inspiring love stories. Anyone actually familiar with those stories should be screaming Critical Research Failure, right? Well, later Ms. Fieldmouse also mentions Romeo and Juliet, specifically calling out the tragic ending. So it's clear that the writers knew the stories but were deliberately using the dissonance to paint Jacquimo as a ditzy romantic.
The fairy brings the old woman a flower bulb that contains Thumbelina. The fairies apparently come from flowers as well. Thumbelina gains wings at the end of the story just like the other faries. That means that Thumbelina could've been a fairy all along, and the fairy woman knowingly kidnapped her from her people.
It wasn't a fairy the old woman went to, it was a good witch. She just looked like a fairy, but it was probably a glamour spell, as witches are known to do.
Mrs. Toad's actions become a good bit more disturbing when you know more about the fine tradition of bridal kidnapping.
The plot in general is a lot more disturbing when you consider that it consists almost entirely of a naive girl being kidnapped from her home and being used and tricked by nearly everyone she meets (even the bird is too obsessed with being a Shipper on Deck to get her safely home). And a lot of those people want to marry her, even though they're different species.
Just...the fact that she isn't given much of a choice whenever someone "proposes" marriage to her is also pretty shiver-inducing. Cornelius had the decency to ask her and gain her willing acceptance first, but both the Toad and the Mole treat it like they're entitled to have her just because they like her. Her agency in general is taken from her at nearly every opportunity.
The level of sadism in Ms. Fieldmouse and Mr. Mole. Ms. Mouse delivers the news of Cornelius's supposed death in the cruelest way possible, and taunts Thumbelina about it constantly, urging her to sing a "romantic" song for Mr. Mole. While Thumbelina's still going through that, Mr. Mole shows her the corpse of her best friend, treating it like an interesting discovery and happily saying "That's one less bird twittering up there." Also, Mole has bugs pinned to his walls as trophies or decor, and Thumbelina has interacted with bugs. So from the perspective of the non-human characters, Mr. Mole's walls are lined with corpses of dead people pinned up for decoration, and finds the accidental death of a man he doesn't know amusing. Also, he was holding his wedding ceremony in the cavern filled with dead-body decorations.