Oh, let me clarify, I didn't mean that Skyler being written as an annoying character is necessarily a flaw. I don't know if it was intentional, but to me it feels like it works well within the story, and makes it feel more real to how real life often works out.

There are plenty of all around good people in real life who just happen to be annoying to interact with in certain contexts. That's just the reality of life, and imo the show executed it well.

I mean, one might take the couple most prominent women in the show being annoying on the one hand and frustratingly bone-headed on the other (Marie) as bias or misogyny... except that nearly all the guys are monsters, or worthless, or are also annoying (sometimes all three). I think it's just a show where almost no-one's good, all the way, entirely, or has always psychologically got it together. Even Hank gets pathetically sorry for himself and starts wasting money on his weird clearly-coping-for-something (ahem, PTSD, among other things probably) rock collecting (well, rock buying) "hobby"—except, I've seen people behave almost exactly that same way in real life! Its characters are human, often such that it's hard to fully like them, just as it can be hard to like most people in real life without some familial or long-running friend bond to get you over their quirks and weaknesses.

... still, there's a lot of time in those first couple seasons in particular when, to the viewer, Skyler kinda just comes off as a clueless nag, even when she's actually behaving reasonably, just because of how the show's presented. "Skyler, you don't get what he's dealing with, just back off!" you want to yell at the screen—then, if you think for a second, you remember he's dissolving bodies in bathtubs and living a secret life and lying to everyone and putting everyone around him in mortal danger and all kinds of messed-up shit, all because he couldn't swallow his pride just once for the sake of his family, so maaaaaybe we should go easier on her. But the presentation, the writing—it does tend to raise such ill thoughts of Skyler to begin with.