Tell me. Here's some of mine:

Asuna from Sword Art Online: Gets hated for being a damsel in distress even though she tried to escape. And because she's an overpowered tsundere. 
Suguha Kirigaya (SAO): Gets too much hate for getting in the way of Asuna and Kirito and for having big chest and falls in love with her brother.

Sakura and Hinata (Naruto): Both get hated on for getting in the way of Narusasu. And both are considered ugly and have zero character development according to the fandom.

Madoka Kaname (Madoka Magica) : Considered weak until the last episode.

Sayaka Miki (Madoka Magica): Was mean to her friends and is considered a "wannabe hero."

The entire cast of Romeo x Juliet: Trust me, the fandom isn't that big. And the characters (that aren't evil or bratty) are likable. But the anime is underrated and so are the characters. Most of them have ONE FAVORITE on MAL.

Lisanna, Juvia, Erza and Lucy (Fairy Tail): Lisanna gets in the way of NaLu according to the fandom. Because of how the fandom sees Lisanna is the reason I hate NaLu. And people hate Juvia because they have a crush on Gray and hate how she stalks him. Erza has some haters for being overpowered and a "Mary Sue." And Lucy's considered useless.

Haruhi Suzumiya: Wow, people hate her because she's loud-mouthed and is a bully? Those are good reasons to hate her but I like how she's not afraid to be herself.

Dawn and Pikachu (Pokemon): I can't believe all those people find these two  'annoying.' They're not all that annoying. Misty was kinda annoying in the first season and so was Ash, but in the next season they're not as annoying.Dawn's not a Mary Sue. She can be pretty demanding when she doesn't get what she wants.

The list goes on and on