I really don’t agree with your characterization there.
Her name might be weird to us but this is an alternate future with aliens so a girl being called Michael is not that strange. Nor would I say it’s a calling card of a Mary Sue. She doesn’t have any unique powers at all either. She’s just flat human woman. Being related to a previous character also isn’t really the hallmark of a Mary Sue. As for no flaws, she has an enormous amount. I would also say that she doesn’t even have a dislike of authority. She has a problem with managing her own authority and overstepping others. When given an order she’ll comply, mostly. There are a handful of instances in which she doesn’t and there are massive repercussions for that. Her flaws run pretty deep. Emotional insecurity and emotional instability due to her upbringing. A problem with not knowing when to stop to the point that she has endangered herself or the crew on a few occasions. She makes rash decisions. She doesn’t ask for help when she needs it and she often rejects help when it’s given. She will take on responsibility for herself that is unnecessary. Spock even makes fun of that in Season 2.
Also the bit about flaws that are supposed to make her more endearing. I honestly cannot think of a single example of any of them throughout the show, especially when everyone reacts to her with utter hatred. I didn’t like her either at the start of the show but that’s sort of the point. She’s built as a character that’s meant to be redeemed, to start off at a low point and an embarassment and to see their character development. Shows don’t work like they do 30 years ago. Characters can’t really come fully formed in an episodic TV show. You need to leave room to grow. Starting off with a character that was fucking up catastrophically is honestly not that much different than what they did with Barclay. It was just done on a larger scale.
I also disagree with the characterization of ‘Mary Sue’ because she’s not the sole person to fix everything. She has never been the sole person to fix everything. She is a person who fixes things but she’s a part in the machine. Throughout Season 3 and 4 you get to see a lot more of the other crew and spend time with them instead of Michael, but they were still there making the massive decisions that made an impact in Season 1 and 2. We just didn’t know them as well. If anything, Michael is the antithesis of a Mary Sue simply because she’s the person who causes so many problems in Season 1.
Honestly I don’t think you’d like Season 3 or 4 if you already seem to hate every fiber of the character.