The problem with rooting for characters to the point where one MUST win for you to be satisfied, is that you're not following the story the storyteller is trying to take you on. The show has constantly tilted one way then the other to get you to root for certain people in certain situations. At the start it was all Walt, and Skyler was presented as the opposition (like Brwned has talked about) and then it tilted the other way. Early on in this season you're tilted towards rooting for Hank, who's presented as broken and faintly pathetic, but then in the last episode, when he dismisses Jesse's life, you're encouraged to tilt away again while Walt displays his desire to protect him. Mike is initially presented as a bad guy opposing Walt, then a good, loving grandfather who Walt fecks over, so when he does it's a big deal. Even Gus is given a backstory to root for at points where the writers want you to be on his side.
So picking a character, and then deciding everyone opposing them is opposing the best interests of the show, and that he must win for it to work is missing the point somewhat. It's fanboism really. And it's also how you get people still hating Skyler deep into season 5.
As long as the show gives you a reason why it should end the way it ends, and the whole thing is carried off well, it'll work.