No Stupid Questions

I think you're misunderstanding the premise of a Mary Sue/Gary Stu character. A big part of definition is that they are almost entirely without flaw, and are generally (although not always) meant to be an author's self-insert. Light and Tony Stark for example, are both intelligent but also stubborn, arogant, privileged assholes who are practically defined by their flaws. Superman could be considered a Gary Stu, esspecially in some of the earlier and simpler iterations but he's honestly such a simple character in general that his lack of flaws doesn't stand out.

The examples that do come to mind are Kirito from Sword Art Online, some versions of Batman, or Butcher from The Boys comics specifically. These are characters that are portrayed as unambiguously good, near perfect men who win every conflict are uniquely capable of solving every problem. Kirito is almost universally disliked, Batman depends a lot on the iteration but generally isn't well-liked as a character, and I've heard nothing positive about The Boys comics (although its less popular in general).

As for why there is more criticism of Mary Sues, I think its not directly because people are harsher on female characters (not that they aren't) so much as because they're more common, esspecially in popular culture. Writing fiction is more cultural acceptable for young girls than young guys, so you end up with more amateur writers writing Mary Sues. In professional projects (notably often led by men due to industry sexism), it tends to be a matter of design-by-committee where they pick a man as a lead to match the male majority, and just throw in a token strong woman as an afterthought.

Now, not every character or show has to be relatable. Peter Parker works because he’s an everyman; however, the opposite can also be true, and people like fantasy escapism. That’s why soap operas about wealthy people or sitcoms about financially stable families are popular, because it’s a form of escapism this goes for Mary Sues and Gary Stus too.

I think a big distinction here is where the enjoyment comes from. You can have a story with a Mary Sue/Gary Stu that is still enjoyable, but generally that specific character adds nothing to the story themselves. For example, if you enjoy Sword Art Online, its for the setting, or the action, or the self-insert-fantasy. Its not for Kirito, and any time you put any focus on him, the story gets weaker. Compare that to, for example, Light, who has meaningful moral complexity despite his unmatched abilities, or Saitama, who despite his infinite power is made relatable through his struggles of daily life. The problem with Mary Sues/Gary Stus isn't their power or self-insert nature, its the focus on a character who is flat, incapable of growth, and/or trivializes any plot.