It's so cute...not.

The aforementioned Teddiursa always comes to my mind for a topic like this. I remember Misty falling for its charm, until the rest of the group figured out that seemingly adorable Little Bear Pokémon was the one stealing everybody's food, including from Brock's backpack.
Another character that would fall under this category would be Molly Hale. (!) Despite being so cute and charming, she did cause a lot of havoc around Greenfield, but you could sympathize with her in a way since she became lonely when both of her parents disappeared, and all she wanted was to be happy for once in her life (which is why she turned her home and the surrounding Greenfield into crystal, and even dreamed up two older forms of herself).
Only a big-time Molly fan like myself would go so far as to whitewash what she did and focus on how adorable/cute her three age forms were.

I remember Delia calling Mimey cute when she first gets him and I thought "Sure, if you say so." I know it wasn't pretending to be cute, I just find that Pokemon generally creepy.