Well, the problem is the game keeps thinking it's a movie and that it's okay to just declare, "This is your best friend. You like this person. You are going to do this ridiculous and stupid mission for him because you love him." I think Infamous deserves the latest prize for this by having the most obnoxious best friend I've seen in a game in ages.
The best relationships in games work just like they do in real life. I meet the person, I spend time with them, I get to know them. Yorda, Alyx Vance, Jenny from The Darkness, all of these characters are distinguished by the fact that the player spends a lot of time working with them. No presumptions are made about me liking them right off the bat and often you have to work with them for selfish reasons. But by the end of the game, it's hard to not have a soft spot for any of them after they helped you out so many times.
It doesn't have to be a lot of time either. I was pretty intent on putting a bullet in Uncle Paulie's head and all I did was watch a movie with Jenny.