@Noah Brode, I hope you know that you've got a lot of good stuff here already! I wouldn't be taking the time to learn the piece and give you detailed feedback otherwise.
Anyway, here goes for the second movement:
II. Thumbelina's Home
My biggest observation about the movement is that the ends of sections generally feel a little abrupt to me. You might consider extending the final chords of some sections so they dovetail with the pickups to the next section. With a little more flow between sections this movement would come together nicely.
The next biggest observation is the handling of chromatic spellings. Reading some lines as a performer, it's not clear to me what the tendencies towards resolution are for some of the chromatic alterations. For example, in m. 5, aurally that is very obviously a leading tone to A, but the spelling of Ab obscures that. G# would make that clearer. The B-flats following I would argue are A-sharps since they have a pull to B. (That said, I don't see a problem leaving the Bb for the harp since that makes the vertical sonority clearer for them.)
Regarding the triplet flurries at B, I can't say I agree with slurring them by triplet. That would make sense for the strings, but in the woodwinds would break the line up more than I think you want there.
Also, in these flurries, be aware that the notes below G4 on the Oboe are heavy and reedy. Synth patches don't illustrate that well.
Given the range of the Bassoon from rehearsal letters B to C, it should be in tenor clef, not treble clef.
At C, you might want to think about bringing the Oboe down an octave. You'll get a richer, reedier sound that may suit your con amore mark better.
Great use of the Horn at m. 99! I wish I had a horn with me here to play that line.
That said, a live horn player will probably produce more of a hemiola effect that you might want here. I can see leaving the preceding portion of C in 3/4, but I really do think m. 99 to rehearsal D would be better set in 3/2. The same comment applies to the Cello solo after rehearsal D.
You have a balance problem at H. Putting all your brass on the top voice is going to obscure the bottom voice. You might save your lower horns (2/4) to reinforce that nice active bit in the lower voice in m. 211-214. They can continue to reinforce Cello an octave up until they go unison with the cello on the D in m. 219.
At rehearsal J, it's not clear what sort of sound you're looking for out of the trumpets. If it's a big statement, I'd probably put them in octaves for the first two bars so that the first player had solid reinforcement on the high B. The fifths weren't working for me. If it's more subdued, I'd go one only. Either way, just be aware that a trumpet above the staff will project more than the synth brass would make it seem.