Though this isn’t always the case with other writers and stories, I do get the impression of some writers treating certain characters as if they’re so idealised as to be almost unrelatable and even Mary Sueish. As in the idealised reader surrogate that some fans live vicariously through and unintentionally bothering others, which I think’s the true hallmark of a Canon Sue.
As for Kitty Pryde, this isn’t to say she lacks flaws (she does have a habit of losing her temper to the point of being vindictive and ruthless that some stories do play up the ruthlessness) but I have a feeling she’d actually be less Mary Sue if she’s less idealised girlfriend/reader surrogate and more like what Psylocke and X23 ended up as: a ruthless ninja.
(Kitty Pryde got trained to be a ninja, Psylocke only got ninja skills through a body swap and that’s saying, as if writers ironically forget canon at times.)
Not to mention, she does have a habit of losing her temper and even violent that the Age of Apocalypse version played up this trait as a ruthless assassin or at the very least, an antiheroine who’s as practical as she’s conniving.
(Actually if they portrayed Kitty Pryde as more of an antiheroine, that actually involves taking her to where she’d logically become like a ruthless ninja who uses the focused totality of her intangilibility and also somebody who’d bend the law to her own will when the situation suits it.)
As for other characters, I still think flawlessness doesn’t always make a character Mary Sue but rather a form of vicarious fan identification that makes it harder to not idealise that’s often different from your usual semi-autobiographical character fiction.
(I did have a Mary Sue character when I identified with a certain character before.)
Whilst not always the case, there’s the problem with trying to turn Patty Spivot into Barry Allen’s girlfriend but because Iris West is his girlfriend the longest and the one with a deeper impact (I always said that the storyline where Barry’s doppelganger kills her and Barry himself avenges her got repeated in later stories).
It could even be argued that Iris West might have more in common with Barry than Patty does that if writers did depict Patty as obsessed with romance novels, gambling and soap operas but Barry’s into hunting, reading comics (Patty doesn’t like that) and the occasional soccer then that’s proving my point right.
Possibly the case with canon to some extent, but that involves realising that either Patty’s not that incompatible with Barry or if she didn’t make a big impact or whatever. (But it could be argued that some writers do depict her as an idealised girlfriend figure, even though there’s the possibility of her liking romance novels much to Barry’s chagrin.)
Both characters aren’t necessarily Mary Sue because of apparent flawlessness but risk being Mary Sue due to over-eager fan idealisation that keeps them from going where they’d logically become or in some cases, be human even if that’s not always the case.