The opinion in the OP is definitely one I agree with, especially this line
Not bad; not bad at all.
But to be perfectly honest, it's an opinion that most people tend to agree with and one I've heard a lot already, so I was gonna play devil's advocate...but @Oriflamme already got that covered. ^^; They even used the Superman example I was gonna use (btw, I think Superman is a great example of a hero who's both OP and extremely moral, yet still manages to be interesting).
So I suppose now all I have left is Option 3: the analytical approach.
I think the issue of boring OP protagonists comes down to a mismatch of storytelling styles, similar to what @Oriflamme explained. Overpowered characters work well in stories centered on philosophical arguments and big sociopolitical questions...they don't work well in the basic anime-hero journey of beating a series of difficult opponents until you make it to the "final boss". Like you said, there are no stakes...because the only stake in a story about fights is the risk of defeat, and if there is no risk of defeat because Protag-kun is unbeatable-- oops, there go the stakes. ¯_(ツ)_/¯
All that's left for the story is either (a) comedic/likeable characters, or (b) a pure unfettered power fantasy for those who are into that. A compelling narrative is pretty much out of the question, unless you change the storytelling style and priorities. So why don't people just do that...? ^^;
My guess is that it's difficult, particularly for amateurs who don't see beyond the surface level of the traditional 'anime-hero' tale. They'll watch something like Chainsaw Man and only see the sakuga and blood and gore, not the biting social commentary underneath the character concepts...and then they'll go to write their own stories and focus on the same things: the cool visuals, the cool powers, the cool protagonist who they always want to see win (so naturally they'll assume the audience wants the same thing)...and before you know it, you have a story that's all tropes and no substance.
Which fundamentally doesn't work...unless you happen to be a person who doesn't care much about substance to begin with. Unfortunately, I think a lot of anime fans are. :T
It's infuriating, fascinating, and confusing all at the same time, and I really want to be wrong...but I truly feel like anime gets uncompromisingly glazed in a way that most other media doesn't. Fans tend to focus on spectacle and nice-looking visuals, and give everything else a pass.
So in an environment like that, naturally a lot of style-over-substance is gonna proliferate; this is just one of the prominent flavors of it. 'Brilliant' strategy just isn't that important when 90% of the audience is satisfied with pretty characters and flashy fight scenes.
With all that said though,
I gotta say my favorite is Spider-Man. ^^ If you think about it, he has a really weird concept...I mean, you're really gonna use the bug that sits in a web all day as superhero inspiration? ^^; And his 'spider sense' is the only spider-related superpower he actually gets; for everything else he has to rely on his supernatural strength and his natural brain.
And this strange, oddly-limited character concept gave rise to one of the most inventive, enjoyable characters I've ever seen; the one and only mainstream superhero who actually managed to capture my heart as a kid. ^^ Just watching him use his webs in creative ways, and take down frightening, intelligent, wealthy adult villains despite being a broke teenager that no one cares about-- he's the quintessential underdog, a character people can't help but root for, because he has to work for everything he achieves. A Spider-Man who is just good at everything and/or gets opportunities handed to him isn't really Spider-Man; the struggle is an essential part of the character, and it's what makes him so relatable.