Wow, I can't imagine how much backlash there would be of Peter dying on Ultimatum, his being the only comic in the line I heard people actually liked.
That is a fair question. I did not read enough about him to know.
But let us check the big parts of being a Mary Sue.
Everyone important in-universe loves them or is, at most, neutral.
As far as I know, the only personal villain for Miles that wasn't inherited from Peter was his uncle, and even then it wasn't a hate thing. And didn't he sacrifice himself for him?
And Miles' survival comes from giving a hamburguer to the Molecule Man, if I remember right. And wasn't he the only survivor from the Ultimate universe because of that?
Lack of any important,
relevant flaws.
Peter was awkward and with a messed family life, used to be poor - and constantly is in need of money, gets no respect as Spidey and is outright feared sometimes, and just has bad luck. Plus everything involving his clones, including his daughter either being stillborn or kidnapped and never mentioned again, and the deal with Mephisto that erased his marriage from existence - including said daughter if she DID get kidnapped. And then there was that whole thing with having his body taken over, and becoming an outright criminal after Civil War...
Peter had a bad life.
Miles... the only bad part of his life I am aware of is the already-mentioned uncle. Plus guilt from when he made a deal with Mephisto and someone ended up dying, which by the way...
The character can do nothing wrong. Not for real, or at least not for long.
Peter... is a mess. Some of his enemies are a consequence of his actions, like Venom, and so many times he made bad decisions and almost gave up being Spider but didn't. Finding and capturing Sandman's
soul. And in the old stories, how people said Peter's catch was what broke Gwen's neck, to the point that at the start of the clone saga when he saved Gwen's clone he acted as if he
did, going out of his way to catch her during a swing instead of webbing her, so making the theory canon. Not to mention the consequences of his choices in Civil War and the deal with Mephisto.
Speaking of a deal with Mephisto, the only thing with bad consequences I remember coming from Miles was his own deal, and it was more that he made a deal to turn back time and save a bunch of people, including other teenage supers, but he failed to save a girl he had the first time around.
Lack of growth and development needed.
Outside Enter the Spiderverse, and I think a cartoon series based on it since on the episode I saw on tv there was a Gwen even if not Spider yet, I'm pretty sure Miles didn't get much more growth needed than actually getting field experience.
Similar to Star Wars. Luke went from a naïve farmer to the jedi we saw through three movies, and we saw his growth as it happened even if it was quick from natural talent. He even needed to be saved on the first movie, and lost his first lightsaber duel in the second. Rey was able to use the Force and stand on her own against a trained lightsaber fighter already in her first movie, with zero actual training.
Now, as I said I did not read much of his stories. He may be more than what I heard of, or he may have gotten better recently.
But at least from what I heard of, he is just... bland, and I completelly understand people thinking him a Mary Sue.