Alternate Aesop Interpretation: Many people thought this was an allegory for anti-abortion. It's not. It's one for Fascism, corporatism and capitalism.
Awesome Art: The visual development team went to great lengths to recreate Seuss's 1-dimentional drawing style for CGI and boy does it show, from the rubbery characters to the oddly-proportioned buildings with inexplicable wrinkles on them, to the various nods to Seuss's entire body of work.
Awesome Music: "Mountain Chase." The temp track for the sequence was "The Ecstasy of Gold", and you can definitely tell the influence. It can easily be mistaken for something Morricone himself wrote.
All the Whos live in a Small Secluded World that can only communicate to the outside through limited means. The Mayor's wife, Sally O'Malley, who's voiced by Amy Poehler, says that she doesn't know the feeling of being watched by a giant elephant. Seven years later...
Misaimed Fandom: Many pro-life people thought this was an allegory for anti-abortion. For one, Dr. Seuss was pro-choice. For two, Dr, Seuss's wife mentioned it was about fascism, corporatism and capitalism.
Moral Event Horizon: Vlad, who takes extreme pleasure in trying to break Horton by dropping the clover in the giant field of identical clovers.
Kangaroo having Horton roped, caged, and essentially tortured, over what she thinks is nothing but a speck.
A deleted scene shows that Kangaroo would have had the Wickershams burn Horton's house down over the speck.
Older Than They Think: The film got an understandable backlash from Seuss fans for modern references like "Who Phones" and "WhoSpace," presumably unaware that Seuss himself made references to computers in his later books.
The Scrappy: Yes, the Kangaroo's the main antagonist, but it seems like she's going out of her way to be the most unlikeable character, be it the book or the movie. Seriously, inciting a mob to torture Horton just because he won't give you the satisfaction of making you think you're right?
Not to mention when Vlad suggests she give him Rudy to eat in exchange for his services, while she decides against it, she still has to think about it for a second.
What Do You Mean, It's Not Political?: Pro-life activists think this book was anti-abortion. Not only was Dr. Seuss pro-choice but the book was published two decades before Roe v. Wade. According to his wife, the central allegory is about fascism, corporatism and capitalism — "a person's a person, no matter how small" refers to big shot governments and businesses stepping on the common worker. At one point a pro-life group actually tried to use the line as their slogan, until Mrs. Geisel sued them.
It's also an allegory for how the Japanese were being treated after WWII; the book is even dedicated to a Japanese friend, Mitsugi Nakamura. There's shades of The Atoner here, as during the war Seuss did his share of anti-Japanese propaganda cartoons which he came to deeply regret.
It works as an allegory for Isolationist foreign policy too.