I have no problem with her. In fact, I think the whole idea behind Skye is that she's not as smart, capable, and all-knowing as she thinks she is. She's cocky and opinionated, but she's out of her depth and needs to learn humility. She thinks she's ready for anything, but stumbles when she has to live up to her boasts. She thinks she has all the answers, but at least half the people on the Bus are wiser and better at this than she is, and she usually ends up being the one who has to learn something. She thinks she's hot and has a shot with Ward, but Ward ends up sleeping with the woman who's old enough to be her mother. So I think you're entirely wrong to assume that the creators are somehow blinded into thinking she's more impressive than she is. She herself is the only one who thinks that, and that's by the creators' design.
I think a lot of the people complaining misunderstood Skye's role in this episode. They showed her acting as if she was the only one who could connect with the safety inspector lady, but I think that was a bit of an intentional fake-out from the writers. Because May was able to get an actual personal connection going at the end between Tobias and the safety inspector that resolved the situation.
Perhaps the point of Skye's actions in this episode were to show that May is an actual human being too. They showed Skye intending to do something, but then they showed May actually performing the task in a manner that would fix the problem.
(Though I'm not sure that sending that guy to hell should actually count as fixing things.)