Let's use X-com as our example canon, Enemy Unknown, of course. If there was a hypothetical fic where the sue in question is a squad member, I would look largely at ease of success. In X-com, tactics are everything. Good tactics can let a recruit (Accuracy of a Stormtrooper + life expectancy of a redshirt) wipe out a squad of mutons (quarter-ton slabs of bulletproof muscle), as long as you're very lucky, and very clever about fighting them.
However, if the sue just walks out into the open, guns down three mutons, and then destroys a sectopod (Huge, well-armed brick powered by pure spite) without even getting close to dead, that is a pretty clear-cut example of someone being overpowered. So, what about a more ambiguous example?
If the sue in question does the same thing, but is not a recruit, and has at least mid-game equipment? A bit more reasonable, as I have had my own soldiers do even more insane things before. The moral of the story?
If the sue in question does everything to stack the deck in their favour, and gathers intelligence, fights like a massive cheap-shot and gets lucky? Well, then it might not be a sue we're dealing with, but rather, a perfectly reasonable character given the circumstances. In that case, the over-poweredness might be intellectual, rather than physical. After all, bringing a gun to a sword fight will ensure your victory, but you'd need to know it WAS a sword fight, or something similar enough, ahead of time to prepare.
In short: If they fight like Superman while still being weak, than it's a sue. If they fight like Batman, it's a bit more reasonable, but you should always be on the lookout for Mary Tzu type characters.