This is something that has been on my mind a lot ever since adopting my cats in July of 2012. They're now in their 9th month, and Biscuit my dilute tortie American Shorthair seems to be regularly dominant, though she's quickest and has the most energy of the three.
They're all from the same litter, but she's little compared to the other two and whose cerebellar hypoplasia wasn't ever as bad as the rest of them. They were the last 3 to be adopted, and I took Biscuit away from the other two first for 2 months, then took in her siblings Bella and Gandalf later, and they didn't even recognize each other,
Gandalf is the only boy and does not like to be picked up, nor scruffed; I do feel an alpha something about him, he's just normally pretty apathetic about things unless he hears a catnip shaker mouse. Or treat bag.
And then there's Bella. She started out very, very timid when she first came to live with me. So skittish, she'd run away if I merely got up from sitting, or if I walked near her. I'd have to turn my back to her, so she would feel comfortable enough to stay put as I walked beside her.
She was getting bullied by Biscuit fairly regularly, but I made sure Biscuit had proper prey to hunt and jump at with toys. Biscuit and Gandalf would play "at her," jump on her, and she'd just want to leave. Now she plays back and can hold her own. I also set Bella on top of their cat structure, I pet her specially, I speak to her a lot, and now she's quite vocal around me and much more confident about her own identity amongst the other cats. If she's at my feet, she'll mew to tell me she's there. She's still the cautious one, the smartest one, the most affectionate, and I'm always working to give her opportunities to come up out of the bushes, so to speak.
She has made a lot of progress and things are actually more equal between the three of them than I think is normal, but the way things are going make me very happy. Before, Bella wouldn't even go up to the collective dish to eat because the other two were there. I would have to pick her up and set her at it, sometimes even feed her by hand. Separate dishes didn't work either, I wanted to integrate the 3 of them together as a family again, so shutting them in different rooms didn't solve my problem. Eventually, she realized her place was with them and not underneath them.
Raising comfortable, confident cats really is the job of a loving parent.