I love how in Vince Gilligan shows, they make you hate the characters you're traditionally supposed to sympathize with and love the character's you're traditionally supposed to hate.
I am a bit late to the party, but I am just finishing up BCS. I hate Saul, and I hate Kim at the end of it all. The way they repeatedly chose the dangerous/destructive path was exhausting and infuriating. I wanted to dislike Chuck, but in the scene where Jimmy got sworn in, he seemed like such a caring and protective brother. That one scene changed my whole perspective on Chuck. I don't think Jimmy is a bad person, but he is clearly deeply flawed and self-destructive, and Chuck was just fed up with his character flaws like I eventually grew to be.
I also appreciate that we got to see more of Mike's back story. I did not really like Mike as a person in Breaking Bad because he was just so cold and harsh. I saw from the BCS, though, that he really was a solid guy with a good heart.
I hated Lalo. He was a complete psycho piece of crap, but I love that they kept with the irony by making him an upbeat and personable personality.
Nacho was by far my favorite person. Even though he worked for the cartel, he had a good heart. He clearly tried to do as little damage as possible, even though his vocation was inherently harmful. I cried when he died.