It's because many people side with Walter. Which is a disturbing fact.£
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Yeah, the big complaint with Skyler is that she's "getting in the way of Walts ambitions", when she's taking mostly completely rational approaches to having to deal with his actions. Like how no, they can't just spontaneously have millions of dollars with no explanation, how they need to keep the story straight and appear legitimate, and how Walt might have to take a few blows to his pride (i.e. the gambling addiction cover) in order to actually sell it.
I always understood that and I never hated her. I only disliked her at times because of how obnoxious she would get. Walt is still very likable in the earlier seasons so it kind of brainwashes a portion of the audience into siding with Walt when she's going off on him 24/7. But it's all perfectly understandable. Once we see that Walt has clearly become the villain, even over Gus, there's no excuse for disliking Skyler in my opinion. Over anything. Even if you were annoyed by her in the past, I think you should be able to "forgive her".
BCS had the benefits of hitting the ground running, having a more concrete conclusion already set in advance since there is a definitive point where Jimmy must, at some point, become Saul. And some of the best moments in the show come from the fact that we know where he ends up in Breaking Bad: when Chuck