3. Skyler
Okay, so Skyler is far from the biggest sinner in Breaking Bad. But lets face it; you want her to die just as much as I do. Its not because Anna Gunn is a bad actress. Its not even because of some questionable decision Skyler has made. Its far simpler than that. Skyler has been Walts most frustrating physical obstacle. Walt has been up against some big antagonists over the course of the show. Gus and the DEA have been his biggest threats. But the only one that Walt has failed to truly win over (so far) has been Skyler. She constantly foils him and we have yet to see him have a definitive victory. We know that, ultimately, good will win and Walt will get what he deserves. But that doesnt change the fact that fans have come to dislike Skyler as an antagonistic force in Walt's arc. Shes been a foil for him and, even though it isnt natural, we as the fans have to root against that foil. So if Gilligan wants to please us, he needs to take her out. Besides, shes far too deep in it now to get off easy.
2. Hank
This is easily the most unfortunate entry into this list. Hank is the only one here who doesnt deserve to die. Honestly, Id like to see him live. But Breaking Bad doesnt always play nice. Remember Hugo the janitor? That didnt work out so nice did it? Hank has been an incredibly surprising character. He started out as seemingly lame comic relief. Since then we have seen him suffer through post-traumatic stress after he saw the real life implications of the meth industry he fights against. Now we have watched a tremendous arc, in which he has become obsessed with catching Walt's elusive alter ego Heisenberg. He is going to be a massive thorn in Walt's side in season 5B. It is clear that Hank is going to be the prime antagonist of this season (or anti-protagonist if we choose to see Walt as a villain). Even if we are building up to an epic face off situation in the finale, Hank is unlikely to survive. If Walt is going to use that machine gun we saw in the first episode of season 5A, it means that he is involved in serious trouble. Therefore, Hank is too. Somehow I think that means we wont be seeing him get that dream job in Washington after all.