I sometimes think some characters tend to be Mary Sue’s because said authors are afraid of making them go the logical/consequential way but that involves taking their actions and portrayals into consideration. Most often or not, the logical conclusion’s only there in apocryphal stories. Keep in mind that Kitty Pryde often loses her temper a lot, lashing out at another person, showing a perpetual grudge and even killing somebody.
Add to her being made into a ninja and trained by Wolverine she could easily be an anti-heroine assassin which’s what she was in Age of Apocalypse. That portrayal’s the most realistic she’s ever been but in the sense of taking her canonical tendencies into consideration. Even if she isn’t a villainness, it’s not that she should be highly incompetent but that she wouldn’t and shouldn’t have any issue breaking the law and being amoral when necessary.
It doesn’t make sense for Psylocke to become a ninja in hindsight as she wasn’t meant to be one, let alone for long whereas Kitty should easily pull that one off. But that also involves realising the more realistic/logical conclusion. This is why I consider the AOA Kitty to be the least Mary Sue she’s ever been because it’s actually the more sensible route for her to go to. Especially if that involves having her to necessarily go and fight dirty.
Realistically and parsimoniously speaking, if you’ve got a character who’s trained as a ninja against her will, loses her temper real badly, has no issue killing somebody and has a nasty grudge then Kitty’s this one character who’d easily do cheap shots. If she can ruthlessly hack into computer systems, logically she wouldn’t have any issue fighting dirty a lot anyways (she did canonically to some extent).
But the assassin route’s actually the most realistic she’s ever been. In the sense of going where she’d naturally go to.