At the beginning of season 3 I thought that maybe they could be friends, real friends. Faith understood Buffy in way that at the time Willow couldn't comprehend, while Buffy presented Faith with something she had never had, family. I think Faith needed Buffy, as a friend, as her only friend but the thing is Buffy didn't need Faith. Especially not after Angel's return. I think this is when it all goes to hell. Faith has spent her entire life NOT being needed. Her mother from what we know was a drunk, all drunks NEED is drink. So Faith would have fallen way down on her list of priorities. There is no mention of her father, her relationship with the Mayor shows how much she craved a father figure. Another reason why Faith and Buffy could never really be friends. Buffy had Giles, and she wasn't going to share, having her own father and abandonment issues to deal with.
So here is Faith, having never been given a reason in her life to feel special and suddenly she is the Slayer, The Chosen. Then bam! she is knocked right off her pedestal by Buffy who is not only a slayer but The Slayer...capital T capital S. Once again she is chasing to catch up and try and prove herself good enough. The thing is it can never happen because she is trying to prove herself to BUFFY'S friends, family and lover. They will ALWAYS be on Buffy's side. By now she knows that she is important or at least she should be important and isn't prepared to play second fiddle, so instead of being the second best good slayer she will be the Best Bad Slayer...something that is her own. I don't for a second think Faith was evil. I think she was incredibly sad and lost and filled with a self loathing that would put Angel to shame. If someone has feelings like that festering inside them they need an outlet, its like poison otherwise. Faith didn't have someone to confide in, not really so she channelled the pain through a dagger...not the best career move but she didn't have the family, friends or upbringing to teach her diffrently.
I think Buffy and Angel could have helped her but they were too caught up in their own drama and Faith was too immersed in what the Mayor was telling her. It's a hell of alot easier to be bad then do whats right. If she hadn't shot Angel I think they could have still been friends but trying to kill him was a step too far for Buffy, like she said herself 'Nobody messes with my boyfriend'. Faith called Buffy out and Buff stepped up and I think that kinda surprised Faith, well I suppose a dagger to the gut will do that to a girl. But in a way I think it really really hurted her that someone that she viewed as her only friend could kill her or at least try to kill her so easily.
I think the whole bodyswitch and Buffy going to L.A. had more to do with Angel and Buffy's unresolved issues with him more than her need for revenge over Faith. I don't see it as a real stumbling block in their relationship.
What I do think prevents Buffy and Faith being buds is very simple, Buffy's pride. Her inferiority/Superiority complex tends to come into full effect when it comes to Faith. Buffy feels challeneged by her and doesn't like it. She likes being the leader, the boss but by being friends with Faith she would have to relinquish some of that power. I mean look at the comic, Faith gets a dingy flat for one in Cleveland while Buffy and co get a castle!
After jail and Angel and everything else she has gone through Faith NOW knows her worth, she's not perfect but she's worth saving. Faith needs someone to make her feel wanted, feel needed and with Buffy all she will ever feel is in the way.