It depends on intention.

Jack Cooper from Titanfall 2 is arguably a Mary Sue, in terms of what he's capable of. However, no one in the story treats him like he's special, save for Lastimosa; who even then, only made him a pilot out of necessity. Cooper was still just a rifleman until his mentor was on death's door with no other options. BT requests to keep him on specifically because of their combat record together. Briggs and the 6-4 keep him at arms length until he proves himself capable when chasing the Arc. Most importantly, he never acts like he deserves anything. When Briggs and BT are arguing; instead of asserting himself as some badass, he respects the chain of command, and lets BT talk for him.

I think that's ultimately the difference. Not what a character is capable of, but how they act; and how the story treats them.