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.
Crowning Music of Awesome: "Marry The Mole" may be a bad song, but "Let Me Be Your Wings" is a pretty decent ballad and considered by many to be the best song in the movie.
Ear Worm: The title song, "On the Road" and "Follow Your Heart". Also, "Let Me Be Your Wings" clearly manages to stick to your head after a while.
Idiot Plot: The only reason Thumbelina keeps getting in trouble is because she won't get on Jacquimo and fly home; made worse by the fact that Jacquimo thinks finding the Vale of the Fairies is more important than flying her home, as well.
The song "Follow Your Heart", as presented by Jacquimo, underlines this plot hole to the point of insanity. (Lost in the woods? Just follow your heart. I could help you by flying home, but...)
Jerkass Woobie: Sure, Beetle is a shallow, self-absorbed jerk, but the only reason he's working for Grundel at all is because the toad was throttling him and then stole his wings, effectively blackmailing him. It's easy to watch him get dragged around by his ankle the entire way and feel a little bad for him.
Unfortunate Implications: How every animal is obsessed with her just for being an attractive human-like woman. Grundel and the Mole want company and the Beetle is lustful and one-sided since he abandons her based on what people think of him.