I think you are being overly critical. I don't think SMG's performance has been bad at all.
I didn't like Michael all that much in the first episodes, when SMG was directed to play her as an emotionless dick, trying to out-Vulcan the Vulcans. I think that is what was intended but I also think it made her more unlikeable than the writers planned. She has since grown on me, again as intended. Nonetheless, she is not meant to be cuddly, she is a coldly competent person who is arrogant about it (legacy of her brains and upbringing), although that is counterbalanced by a reckless streak a mile wide (which proves how human she actually is). One of the show's big story arcs is Michael growing into her humanity.
I think SMG has been best in discrete situations when what she is supposed to do is clear. She is great in moments when Michael is faced with a challenge and grabs it by the balls, like escaping the tardigrade, challenging Kol or stepping into the role of Mirror Burnham. She was also good in the scenes with Tyler, when she is facing down unfamiliar emotions and struggling to deal with them. She is less good at figuring out where the character is supposed to be mentally/emotionally in scenes that are more ambiguous or not explicitly about her. (If she wants a master class in how to do that, she can watch Jason Isaacs. The young actors should be watching every move he makes if they aren't stupid.)
Overall, I'd give her a B, and she's getting better as she and the writers figure out where they are going.
Sonequa has both the advantage and disadvantage of playing against a uniformly good cast, every one of whom is capable of outacting her if she doesn't bring her A game. Isaacs, in particular, has decades more experience and is as good an actor as anyone, the first we've had in Star Trek who is fully in Patrick Stewart's league.
Not only is he really THAT good, the part of Lorca plays to all his strengths. It could have been written explicitly for him (and probably was customized to a significant extent after he was cast). It's kinda like hiring Eric Clapton to play the blues, it's no surprise when it goes really fucking well.
And Lorca is SUPPOSED to be commanding and charismatic, that is part of who he is, one of his biggest weapons. He is a seducer, who excels in figuring out what motivates people and getting them to think what he wants is their idea. Isaacs has been working that every minute of every scene. So not only is he the most complex, unpredictable character, he is also being intentionally written and acted to be impressive. It is no accident that I (and apparently many of you) love this fucked up guy.
My bottom line argument is that it is unfair to compare the two characters, and actors, for all of those reasons. I think they complement each other, and I think SMG has done well to not be completely blown off the screen by Isaacs, which she hasn't been.
I fervently hope the writers realize how important Lorca is to this show, and that losing him would blow a big black hole into its center. I think they probably do, though I don't know what their exit strategy is. Have him redeem himself? Have Prime Lorca show up? Bear in mind, we do not yet know that he is actually evil. He may be a freedom fighter. Who fucking knows, this story could go anywhere, which is one of the reasons I love it, but I hope it goes somewhere Jason Isaacs is still aboard because he is the best thing about a show I like a lot.