No it isn't. That's a cheap and easy complaint to make.
Skyler's problem is that she's the only character in the entire show that doesn't actually fit in the show. She doesn't make sense in a show that is inherently surrealistic, because she's a realistic person.
People compliment her for being realistic, but realistic is the wrong choice for her character to be in the show. Every other woman in the show is fine--nobody complains about them--because they fit the surrealistic attitude of the show that has a severed head on a tortoise and a pink teddybear floating in a pool and a guy who shouts THIS. IS NOT METH. and a weird old dude in a wheelchair who rings a bell and Colonel Sanders who was originally a Chilean revolutionary and twins who are introduced praying to Lady Catarina (iirc?) and so on and so forth.
The show is weird. It's dreamlike. There's a strangeness to it.
And Skyler is the person who threatens to make Walter MUNDANE. She is the person who basically wants Walter to stop destroying himself and everything around him. She's reason in a sea of crazy. And we're watching the show for the crazy. We aren't watching it for the sanity.
She'd be absolutely perfect in a show that was realistic and grounded, but that's not Breaking Bad. She doesn't fit in Breaking Bad. She's this consistently jarring character. She breaks the mood. She whines and complains (which is COMPLETELY REASONABLE for a real person to do!) and we're like "shut up, I wanna watch Walter melt a man in acid" or whatever.
This is a show with an episode about killing a Fly.
Skyler White does not fit.
Isn't it possible they're just bad/wrong characters for the things they're in? There are plenty of great women in fiction. I'm a huge fanboy of some sf novels that are majority female lead stuff, for instance. I think Dana Scully is great. There are tons of women in fiction I think are great.
People like Lori and Skyler are very noticeable outliers. There's no misogyny there.
Except for that Skyler is a character foil designed to 1) widen the spectrum of "reality" under which the show operates and 2) keeps Walt as a character and his situations interesting. Some of the absolute BEST moments of the show involve Skyler in some way (directly or indirectly), and I think you'd be lying if you said that it was by accident.
So much of Walt's characters and motivations, even as they evolve, revolve around the people he's most close with. Hell, that's one of the things that the show continued to revolve in, the smallness of the "world" around Walt and how his actions, big and small, have an effect. They (admittedly very clumsily) took it to the extreme with the plane crash at the end of season 2 to really drive home that point. He doesn't get brought down by random feds, it's Hank. He doesn't get into the business by talking to some random kid, it was a former student. The world he lives in, the things he does is directly affected by every character, and that very much includes Skyler and HER actions and reactions to what's happening to her as well. You can't remove her and think we'll get essentially the same show.
So, knowing we can't remove her, we have to work with her in a show that is about a high school teacher cooking meth. He has a family with a wife, a son, and unborn daughter. He has a daily routine as an everyman, comes home at roughly the same time, and just as everyone else, if you act erratically people notice. His wife obviously notices. Walt has to start maneuvering around his daily routine and actions, making up work excuses, blaming his cancer, etc., and between the stress of everything going on around him and the drug business he doesn't know how to handle, he makes mistakes. Skyler doesn't go apeshit at the very first thing that doesn't add up, but rather she grows suspicious. From that suspicion she starts thinking about shit, and from that she investigates. What if she did none of these things? 1) She'd be a TRULY boring character with zero depth and 2) that'd actually be slightly sexist as we'd have a stereotypical dumb housewife who can't think for herself that her husband is in the drug trafficking business.
I agree with your notion that there's an element of the supernatural in the show, but that doesn't mean there's no place for reality. The show is nowhere near as unrealistic as you say it is, and would actually make the show COMICALLY unrealistic is if Skyler didn't suspect of push back against Walt's insanity. Well written conflict is what elevates a show from good to great, and this show had that in spades. To argue you want a Skyler that "isn't a buzzkill" (in so many words) is to argue you genuinely want a worse show.