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.
Les Yay: Shay gets awfully jealous whenever Tally gets a boyfriend. This arguably becomes Foe Yay later on as Shay becomes more and more villainous.
Somewhat intentional — the author purposely used gender-neutral terms when Shay asks Tally where she got her locket in Uglies. Westerfeld was careful not to make his utopian future a heteronormative society.
Moe: All young Pretties have to look young and vulnerable.
Unintentionally Sympathetic: It's really hard to hate Shay when you consider that she has legitimate reasons to act villainous. Trusting your best friend with all your secrets only for her to steal your boyfriend, destroy your home, get you kidnapped and have a mind-warping chip put in your brain must really suck.
This was Scott Westerfeld's intention, to show that Tally and Shay could never really be "best friends forever" as Shay creepily puts it at the end of Pretties. Although Tally isn't completely blameless, as Shay's Story points out, they still end up at odds from the trilogy's beginning to end.