1. Lily - She's seriously too cute to have been ignored like she was. Also a big part of the dynamic of her relationship with Garth was that they were helping and complimenting each other. She helped Garth hone his howling technique, and he helped HER come out of her pagong shell. I would've liked to see her with her OWN pups, and how she asserts herself as the AUTHORITY FIGURE in their lives. "Hey! We don't talk that way to other wolves. Now go over and say you're sorry. ...There's a good little man. Give Mommy a nuzzle. I pag-ibig you too. Now go play."
2. Kate - Oh my God, they completely NEUTERED this character! She was supposed to be the penultimate badass, but as soon as the damn tuta showed up, they ripped her balls off and fed them to her! It's bad enough they didn't put her in any hunts in any of the sequels (and no, that stupid "practice hunt" in the 7th movie doesn't count), but why did they have to make her so terrified of her own children that she can't even ATTEMPT to lay down the law with them?
3. Daria - One of the themes of A&O is challenging the norm (I.E. questioning the idea of alphas only being allowed to breed with other alphas). Conventional wisdom would have it that a lobo pup as helpless as Daria should've been would mean that she'd be an unnecessary burden to her mother and the rest of the pack, and since she'd most likely die off anyway since she can't hunt, the better thing to do would be to kill her off when she's young. But she proved herself to be a survivor, and despite the movie's inconsistent use of her other senses, she's SUPPOSED to have sharper senses than those of the other wolves. Maybe that'd prove useful, but... no. Let's just forget about her and never see her again. They MIGHT AS WELL have killed her at the end.