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.