Exodus is when I really think her character's going to do a 180 over the next few seasons. She's dealing with her grief and pain and fears. She could become very bitter (and she really did seem it next season). Then there was Walt. Walt, this special insightful little boy who seems to know things that could happen and has a psychic attunement to the island, chooses her. Out of everybody else on the island, he chooses Shannon to take care of Vincent. Walt, who loves his dog and regularly runs off into the jungle to find him, gives care and responsibility to probably the least responsible person on the island. Why? It isn't out of respect for her brother's death, I don't think. It's not pitying or consoling act. He wouldn't give care of his best friend to someone just to make the other person feel better. That doesn't seem like Walt. He could've chosen anybody on the island. Why Shannon? He chose her because he thought she was the best person for the job. Yes, the absence of Boone was a part of it, but it's because Shannon would be the best person to love Vincent as Walt loved Vincent. Walt trusted her. He trusted her more than anyone else there even though they had never shared a scene together. And Shannon was touched by it.
Remember when Sayid asked Shannon for help and Shannon rebuffed him because he only asked because she was the only one who could do it? She was the only one who could speak french and so it had to be her? If there was anyone else who could speak French, she'd be completely ignored so it angered her. But this? Almost anyone can care for a dog. Lots of people own dogs and give them happy healthy lives. Walt could have given Vincent's care to anyone, but he chose her.
Between the loss of her caretaker and her shelter, and the gift of trust from a stranger (because that's what Vincent was, a gift of trust because Walt wouldn't give Vincent to someone who couldn't take care of him), Shannon was set to get started on her journey. There were a lot of clues through Locke's few appearances with her that she was set for going places.
Alas, it was not to be. Whether it was fan backlash, a punishment for wanting to be in the X3, or mishandling of the character in Season 2 (which happened for nearly every character), she didn't go anywhere. Even though she was even more whiny and ggravating than usual in the first episode, it was understandable. Her brother's only been int he ground a few days and she's still wrapping her head aroudn being given responsibility of Vincent. She lashes out, it's how she reacts. And even worse for her, there's another La Mer moment when she sees backwards-talking dripping Walt. She doesn't understand it and it makes no sense, but it happened and nobody believes her. Just like the French scribblings were a song. She knows she was right and she's not mistaken, but it makes so little sense that no one can believe her.
I don't know. I really saw her character growing into someone strong and confident later on. It would be a slow process, but eventually she'd be trying things she didn't think she could do before and finding she's good at them and really starting to get involved. She still can see things that make no sense, but people eventually learn to trust her. She becomes a competent member of the society. A leader? No. A Mary Sue? God I hope not. But maybe like how Sawyer developed or Hurley where people are comfortable with her and she does things without the kneejerk self-loathing. She just finds a role in the group and she begins to really love and trust herself, and consequently, love and trust other people too.