The answer is that the pop cultural idea of the young male was stuck glamorizing lameness for a decent chunk of time. Particularly in nerd spaces.
I can think of a good dozen webcomics, ones I love dearly, where the main male character, typically an author stand in, is an ineffective manchild who's greatest asset is his knowledge of pop culture. The kind of dude who wrote Ready Player One, where the main characters superpower is being able to quote movies good.
In that ecosystem, Scott Pilgrim is almost a deconstruction of that character archetype. His viewing of life through video game terms is shown to be an active psychological weight that drags him down (the same way it drags down Ramona and Gideon, who are equally bought into that viewpoint).
But here's the disconnect: to that mainstream nerd dude audience at that time, there's nothing wrong with Scott. If you approach Scott as the standard lovable slacker nerd constructed for you to comfortably ooze your lame-ass self into, then he video game fights and doesn't afraid of anything. He's so cool haha, duuuuude, I wish I had video game powers in real life man it would be so awesome, this is cool as hell I liked when they referenced the legend of zelda its so cool that theyre finally making movies for gamers dude.
When you're reading from a position of entrenched and comfortable mediocrity, you don't read that character as a critique, because youre used to laughing off all of those flaws.
Notably, the mediocre nerd male lead is typically also seen in that time frame as an underdog, because his assets are whedon-esque quips and knowledge of spider man comics rather than physical prowess or social charisma, as a sort of counterpoint to the mainstream mook male. The nerds of the time were sure that their lame-ass male leads were far superior to the "normal asshole guys", who if you asked them to define, they would probably point to the dudes on jersey shore.
That's also an important part of the whole thing, I think. The nerd dudes of the time did not perceive themselves as a criticizeable party. they were the underdogs. the nice guys. a tortured minority made superior to the drollish majority through their media consumption patterns alone.
So of course they didn't see Scott as critique... they didn't see why anyone would want to critique them or that it was even possible. They had main character syndrome but for their entire subculture.
This is also, I theorize, why they lost their shit when Anita finally showed up on their radar.
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