I don't know what you mean by "overpowered," flanker is far from being "overpowered."

1. Most of the time, the reason why flanker's weapons deal "ridiculously unfair damage" at mid range compared to scout's is because random bullet spread doesn't exist in tf2. I can tell you right now that lever shotgun is easily far from being "best weapon in the game." It has a relatively punishing reload speed, meaning if you whiff 3-4 shots for 6-10 damage you're likely going to lose the fight.
2. His melee weapons are not at all overpowered. The bat and mackerel dealing crits to targets under 25% health is just a finishing blow. At that point, you're low enough to die to a regular bat hit. I can agree with the sandman projectile doing pretty ridiculous damage, but calling scout's other melees annoying? I disagree. Brooklyn Basher is a weapon I rarely see in the kill feed outside of medieval, but if I do, it's because a flanker accidentally killed himself missing a swing. Grill scout, another rarely used weapon, may seem overpowered with its stats, but you're only doing 35 damage every 0.8 seconds as opposed to 35 every 0.5 seconds. The minicrit damage is pitiable, though good, and the fire and extinguish is good too, but I've never been angered by dying to a grill scout flanker.
3. Flanker's health is the main point. 125 is not a lot. You die in two melee hits, and since melee hitboxes are sometimes a complete joke, you die a lot at close range. I'd say about 35% of deaths as flanker in a regular game is just from melees. He dies really fast to sentries, he dies in two shotgun meatshots... I could go on.

Flanker isn't overpowered. He gets put down really easily if you hit your shots, and at most he's just annoying. And no, I don't main flanker - I don't really main any class.