Audience-Alienating Premise: The show is aimed at little girls and is Magical Girl themed, but it also has a surprisingly dark plot and tries to raise questions about semi-serious topics such as love and femininity (with mixed results). It also suffers badly from Most Writers Are Adults, which can be off-putting for a lot of people. Possibly because of this it never really became popular outside Japan and faded into obscurity there after it ended.
Awesome Music: The opening tune "Chocolate ni Muchuu" is a bombastic throwback to songs of the 1970s, and the first ending song "Tsuki no Mukou no Sekai" is just gorgeous.
Awesome Art: The manga has gorgeous and very detailed art.
Base-Breaking Character: Vanilla after she becomes the Ogre Princess, and over whether or not she was Easily Forgiven. And there are fans who just don't think she's as interesting as Chocolat.
The series' social commentary about love and femininity is seen as either thought-provoking and adding depth to the story or clumsily written and making it incomprehensible to non-Japanese audiences.
Should Chocolat or Vanilla have won in the end?
The anime. A lot of fans don't like that it differs so much from the manga.
Designated Hero: Though the protagonists are certainly not as villainous as the Ogres, their habit of harvesting human emotions for energy sounds like an evil plot straight out of Sailor Moon, though it doesn't seem to harm them.
Growing the Beard: A little less than halfway through the series, when it stops being "how to get boys to like you" and becomes a more straightforward magical adventure.
Les Yay: Between Chocolat and Vanilla, expectedly.
Suspiciously Similar Song: The theme song was meant to sound like Serge Gainsbourg's "Poupée de Cire, Poupée de Son" (Wax Doll, Sound Doll), made famous by France Gall when she sung it at the 1965 Eurovision Song Contest and won.
They Wasted a Perfectly Good Character: Of all of Chocolat and Vanilla's classmates, less than a handful get any development or relevance to the story. Most of the time they just act like a Hive Mind.
The biggest offender of this is Akira, who was clearly set up to be a relevant character in the beginning and was even promoted as such early on in the manga, just to get sidelined and be little more than a minor character in the end.
Despite being a major character, Pierre's past is never explored in any meaningful way.
A lot of fans in the west (where tomboyish girls are seen as more desirable) don't see anything wrong with Chocolat's behavior early in the manga and think she's treated way too harshly; on the flip side, the much more feminine Vanilla is played up as the human world's ideal girl. The story also puts heavy emphasis on the idea that No Guy Wants an Amazon, to the point that everyone in the human world agrees with this. This may be the reason why it never really took off outside Japan.
In order to collect hearts, sometimes the girls have to act helpless and/or incompetent. To some outside Japan, this might come across as creepy or downright sexist. Though, at least in the manga, this objective is eventually deconstructed to anyone paying close attention.
(Wax Doll, Sound Doll), made famous by France Gall when she sung it at the 1965 Eurovision Song Contest and won.