While I am maybe focusing on the negative, I am trying to specific enough that it is constructive critism and the key to fixing the chemistry is visible.
I think a recurring problem is most of the writers remotely interesting in making Sally 'flawed' don't really understand the 'quirks' and defining characteristics of her personality. Ian doesn't really grasp Sal's personality, she actually tends to come off rather bland most of the time. Hurst got most of the key shortcomings of her character down pat in terms of her demeanor and acting (eg. well intentioned controlling freak, neurotic, self righteous, finicky temperament) but never really made any story opportunities when they were the focus or made her screw up. He probably made the most accurate case where Sonic 'won' against her approach in Drood Henge, specifically winning because Sonic was willing to take an opportunity and was less overcautious and by the book than Sal, but even then, Sally didn't really make a detrimental error in this case, just found a circumstance her way could overlook key advantages.
Others try to make a similar rendition, but it never quite has the effect, either because it's harbored with pretentious melodrama and angst (eg. the Slap) or actually involves her flip flopping her approach and doing something that is somewhat reckless (eg. Secret Scrolls, the first issue) which in a sense also makes her look a bit like a hypocrite who badgers Sonic over standards she can't hold up to herself. Writers fail to really pinpoint Sally's flaws in a way that don't make her unsympathetic (or when they do they overdo the waterworks and outright make her errors too forgivable, eg. Ian's wangsty moments in the Iron Dominion arc).
I can sorta understand this problem since Sal's approach in a flawed nature would most often make her a control freak, which can often be viewed as very unlikable characters when made in the wrong light. This isn't always the case, but if you don't write their views and feelings consistently enough they can go from a character who merely thinks they know what's best for everyone to something of a self serving bully.
I want you to factor in that she is indeed a child solider and leader with tremendous stress on her. She wants her plans to work, and there is room for fallacy and overconfidence. If we look at people like Tesla and Einstein we see their brilliance was variant and they could suffer from mental tunnel vision. I myself have Aspergers, and though, last time I checked in 6th grade, have an IQ in the high one-hundreds, I have some hilariously dumb moments (usually involving finding lost things that were right in front of my face along, like, in literal sense, my glasses.
) I want you take good note of her backstory as character and her mentality for a sec. Abandon the tropic thinking and psychoanalyze her like a real person a for moment.
I understand, but I feel these are things lost in execution, since not only do they not really focus on her flaws and insecurities accurately enough, they aren't always careful to keep the sort positive well intentioned aspects that drive them evident as well. Most fans were pretty assured the slap was the worst thing to happen to her character for example and her moment in the first issue (while played more for laughs) pretty much played her as catty bitch with a 'Never My Fault' complex.
Also as mentioned they have to be careful which flaws and character traits they stem from. I don't think all these attempts to show her randomly being reckless and cocky work because, not only is it not really connected at all with her own ethics and potential shortcomings, it also makes her look like an enormous hypocrite. Having her make the same oversights as Sonic works for a sparse 'Not So Different' moment to show it's not always easy keeping to standards, but making her most consistent pivot of error going against her normal approach makes her look like she makes orders and standards for people she doesn't try to uphold herself. Same for Sonic giving this like the wind ethic but then holding grudges and having angsty outbursts when the problem concerns HIM. It diminishes the positive elements of their approach and just makes them inconsistent egotists who think everyone should be subordinate to them, rather than just being so passionate and assured of a specific ethic that they get kinda pushy and bull headed about it.
There's also the fact that a lot of times, the humility or consequences that come from it are downplayed. Flawed moments worked if they are treated realistically, but a character who is enabled and never learns from their errors can come off annoying (again the first issue, the reason the plan failed was as much her fault, but she threw a huge tantrum blaming everyone else and pretty much telling them it's their fault their family's are still captive and suffering, to which the others...just accepted it). This is especially problematic because one of Sally's most consistent flaws is that she's kinda self righteous, a trait that can be sympathetic when treated with the right humility, but when enabled constantly can make the character completely insufferable. No one likes it when a character gets an undeserved pedestal.
I feel that in concept her character has all the right points to make her sympathetic in her meticulous aspects (she's traumatized from witnessing people suffering from making risks or errors, her foil is just as pig headed and confrontational as she is, and she is even implied to have been brought up by a strict authority figure who has raised her to trust standards and rules rather than her own initiative), it should be pretty much engraved into her mindset given what's she's been through. The problem is most of these elements, and the flaws that potentially stem from it, are often skewed or overlooked, like the writers don't really know what her actual personality is. She's basically a jigsaw puzzle with a beautiful complex picture when finished, but has been pieced together in completely the wrong way.
