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.
YMMV: Gakuen Alice
Complete Monster - The Elementary School Principal, Kuonji. Kidnapping, extortion, blackmail, child abuse, child slavery, etc. He's... not a good person.
Tear Jerker - Most of the manga from about chapter 90 on (and other situations before that, possibly). Particularly Yukihira-sensei's death, and the aftermath
Title Confusion - The series is called Gakuen Alice, but the school is called Alice Gakuen. The Animax dub simplifies this by calling the show Alice Academy.
This is a side effect of the way words in names flip around in Japanese/English translations. What they should have called it is Xanth Academy. (If you like this series you may just like "A Spell for Chameleon".)
Don't forget Luca and Sumire! (Consider the interaction of their powers.)
Let's just stop here and say that there's a lot.
What about Luca and Natsume?
The Woobie - Mikan, especially when she first enters the school and has to bear plenty of snobbery from the other students and a crappy dorm room. Things gravitate from worse to better as the plot progresses, though she has friends to back her up and protect her heavily by then.