Honestly, you could probably make a case for all of the Scions by the end of Endwalker being Mary Sues if you really wanted to. Here are a bunch of extremely learned wizards who apprenticed under a guy who punched out Bahamut, have saved the world multiple times, saved another world, are friends with everyone, and managed to survive all sorts of stuff that would kill most anyone else. And that's not even getting into the Warrior of Light. But for a story about fantasy and adventure, I feel like you kinda need some extraordinary people to lead the plot, so that is what it is.

Now, as far as what you've said about Y'shtola goes, I think she's a little static, sure. She's the sassy catgirl who throws out dry quips at people. I wouldn't say that alone makes her a Mary Sue, though. Just a bit more simplistic compared to everyone else. If anything, I do think it'd be nice if she stopped flouting her plot armor so flagrantly in every expansion...