She is quite wonderful. The "pointing out that she is in charge" is entirely ABOUT her being/looking like a woman and therefore to be ignored or disregarded. Several of the times, the other people in the story will turn to Graham - the white male - first for leadership. Is "miscast" code for "Bradley Walsh should have had the part"?
I'd say that generally the Doctor is never assumed to be the person in charge of any given situation. He/she will just take the reigns when the circumstances call for it; some recognize that he knows what he's talking about and follow him, but there are always those who don't and usually end up paying the price for it.
I wouldn't say Jodie was miscast, but I do find myself still waiting for that moment where everything clicks and she feels like the Doctor. I had the same feeling about Capaldi though, his Doctor was also rather uneven and it was a long time before he clicked - pretty much right after Clara left. And dynamic between the Doctor and the companions is arguably a very important component. It's been so long with the others that I don't fully recall when they all clicked with me as the Doctor; I think Eccleston took a couple of episodes, even though he was my first exposure to Doctor Who, there was still a settling in period. I believe Tennant took a few episodes to completely accept him as the new Doctor. I want to say Matt managed to win me over right away, but I don't remember for certain. I know for Matt it was his ability to simultaneously be so young, yet convey a sense of much deeper age and the weight of that, that won me over. I think the main thing with Jodie though is the writing, or more accurately the character development or the lack of same. Jodie's Doctor hasn't been given much in the way of her own identity to build on, but instead seems to rely heavily on an amalgamation of past iterations and their characterizations. While not quite as garish, her costume has made me think of 5's patchwork outfit. I feel like there's a touch of 9's manic personality, but it lacks the weight of being "the last time lord" or thinking he'd killed his own people.
Now that I think about it, what might be missing most is the Doctor's arrogance; which is sort of an odd thing to say, I know, but the Doctor is generally the smartest person in the room and knows it. Normally that's not a positive trait, but with the Doctor it's generally well deserved. Calpadi's Doctor had it in spades, perhaps even to a fault. Jodie's Doctor sort of takes her knowledge for granted, and even at times assumes that everyone else knows what she knows...
I still would have liked to have seen Hayley Atwell as the Doctor, but Jodie isn't the end of the world; and would still rather see them find a way to make her iteration of the Doctor a success.
“In the game of chess, you can never let your adversary see your pieces.”
I dunno! Is my decisive and helpful answer. As mentioned before, I see her as Eccleston 2, which doesn't float my particular boat, but that is just my opinion. As also mentioned before, I haven't seen her in anything else, so don't have much idea of her range and style; so for that reason I don't feel I can say she's miscast, or perfectly cast for that matter. Plus, I always feel any Doctor needs two series to establish his/herself. Capaldi, whose casting I was very excited about, ultimately proved a disappointment for me personally, though I felt ultimately the show's runner and writers deserved most of the blame; utterly incoherent and unmemorable stories being the problem with his tenure. But I always felt he needed the second series, so I'm prepared to give Jodie more time.