The first is that of Eric Shellhorn. In his first book, he appears, like his sister, to be an unfortunate little boy, with Venetia for a stepmother. Venetia manages to find spells that turn him evil. The later books treat him like he's evil beyond any hope, which is VERY questionable.
For the first five books, Miss Crystal appears to be a delight, beautiful, sweet, kind, generous, and trustworthy. The fifth book reveals her to secretly be an evil Enchantress. But... She doesn't even seem to retain her superficial charm, which makes her seem like a completely different character. Indeed, it could almost be believed that the real Miss Crystal has been kidnapped, and Mrs Tilpin is, in fact, not her at all.
Designated Hero: Benjamin's parents for most of the series. They cruelly leave Ben on his own most of the time, and have the gall to act like they're better than the more sympathetic members of Charlie's family sometimes.
Designated Villain: Eric, Eric, and did we mention Eric? The little boy was a victimized child like his sister, and was hypnotized to help his wicked stepmother. Never do the good side attempt to bring him back. And did we mention this is a 7 year old boy?
Lyell could also count, in a way, but more in backstory than in the actual series. His father died when he was a baby, and his mother was a complete Jerkass who probably neglected him emotionally once she realised he wasn't endowed in the way she wanted him to be. He spent a good part of his childhood surrounded by nasty, cold-hearted relatives such as Yolanda and the Aunts, and judging from how terrible a sitter Aunt Eustacia was, one can guess how he was treated. On top of all that, his mother held a grudge against him because of a will and a letter his father wrote to him. He falls in love and wishes to marry, but the Yewbeams don't approve and forbid it. He elopes anyway, earning the ire of the entire Yewbeam family. Then, after just four years married and with a two-year-old kid, he gets hypnotised for life when he tries to stop the abduction of Emma Tolly and spends the next ten years in a deep trance, unable to remember anything about his old life. In the fifth book, when he's close to awakening, he almost dies because Harken bewitches Amy into forgetting him, and all because the Bloors and Titania don't want him to wake up and remember where he put the box that contains Maybelle's will. Even after his awakening, Lyell is still not completely himself again, with parts of his memory still missing. Though he does eventually regain all of his memories at the very end of the series.
Emma Tolly was abducted and hypnotised as a baby, and lived a dull and unhappy life for eight years with neglectful foster parents. When she finally wakes up from her trance, she cries and says that she never knew how unhappy she was, and that she lived with people who didn't love her. The happiness in her life only starts when she goes to live with Miss Ingledew in Ingledew's Bookshop.
Paton. His mother was murdered by Yolanda in Yewbeam Castle when Paton was only seven years old; his sisters turned to evil at the same time. His endowment made him a pariah in society and his own family, as he couldn't go outside in daylight. Also because of his endowment he's pretty much a loner, as not many people are brave enough to befriend him. His only friend Lyell disappeared under mysterious circumstances in 1994, and Paton blames himself for it because he didn't meet Lyell when Lyell asked him to. Paton meets a nice lady who he really loves, and who loves him back, but something always seems to crop up to stop them from progressing their relationship into something more.