Yes, I think you're correct.
There are plenty of characters who are incredibly powerful or unreasonably skilled who are still well-liked and don't tend to get the Mary Sue title thrown at them. Batman and Lina Inverse are examples I'd give. What really makes somebody "feel" like a Sue is when the narrative seems to just keep handing them stuff, and they always seem to triumph... while the character and narrative always insist they're the underdog or are justified in being like "Ugh... people are the worst."
A lot of people claim "Well MY character isn't a Mary Sue because he's ugly and dirty and he's a murderer who's hated by society!" but the Sue vibes can come through in a different way, for example, the guys who are after him will turn out to be even worse people, everyone who tries to stop him will be afraid and/or respectful of how dangerous he is, he'll get given a really cool nickname by the police or media like "The Nightmare Killer" or "Mr X", there will be obsessed fans following him around, probably including at least one unreasonably attractive young woman who finds him sexy no matter how much he spurns her, he'll possibly spark a revolution too for good measure. He misses that the thing that makes a Sue really a Sue is that the fictional world a Sue inhabits all believes the Sue is important and somebody to respect and be in awe of, never to pity, ignore or laugh at.