I listened to this right after "For Want of a Nail," and so that colored my reaction. I enjoyed "Amaryllis" -- it's perfectly pleasant and well-characterized -- but it felt to me like this story was really only grappling with one issue (the protagonist's lack of self-confidence), whereas "Nail" was grappling with several (dementia, engineering, the protagonist's youth and inexperience, etc). And the resolution, as other people have said, was pretty simple, with no actual hard choices to be made. I've spent some time considering whether I'm falling prey to the common pattern of valuing certain kinds of stories (war!) over others (love and other squishy things!), and I don't think so; "Nail" was also very personal in a lot of ways, but it was an orchestrated composition, whereas this one is a pleasing-but-simple melody.
So yeah, it ends up looking weaker than it might have if people weren't judging it as a Hugo nominee.