People are just too quick to throw around the words "Mary/Marty/Gary Sue/Stu," no matter how inappropriate it might be.
I think it's worth noting that Snails, despite not being that smart, was the first unicorn child somewhere around the CMC's age range (he and Snips seem to be in their class, taught by Cheerilee) to use even the most basic magic (using it to light up the cave
, in his case, even if he had a bit of trouble), all the way back in S1.
By comparison, Sweetie Belle's magic, for how impressively far it got later (and is therefore a reason to think she's markedly above average), didn't even show signs of existing
and S4 was when she first learned to have even the most rudimentary control of it, under Twilight's tutelage.
So him being above average in his magic in a character consistent way doesn't really seem farfetched to me. He still has character flaws established by S1, so therefore, he isn't a "Gary Stu," it's just adding onto his previously mostly one-note characterization, by giving him a strength he'd developed offscreen over time. …Also for secondary stuff, the comics kinda pointed to the way he was later portrayed in Buckball Season, being useful and all, surprisingly/funnily enough, with how he and Snips had managed to learn a fire spell, among other things they did to help.
It's like saying Starlight's a Mary Sue on the basis of her magical power, despite how she isn't
portrayed as infallible, but that's another story. It's alright to dislike a character, or how they're handled, for whatever reason, but that doesn't make that label true… and it's losing its meaning with how overused it is, if it isn't already all gone.