Well an academy student pulling out 100 shadow clones could very well kill them yes but a Jonin could do it I think. Though I don't think Naruto can do it because he is an uzumaki but because he has the fox in him. After all Karin is an Uzumaki and she can't pull off the stupid bullshit.
... I would argue that him being capable of so many clones due to the fact that he, from birth, got the largest splinter of the closest thing his world had ever seen to a straight-up deity isn't really helping in that regard.
Also the big bads usually also are hard workers. They aren't couch potatoes there are couch potatoes in all worlds and it's not easy to not be one. Also just because the hero beat the villain does not always mean their power level was higher sometimes it could be a temporary thing due to high emotions like when grandma can lift a car to save her grandchildren or it could be bad luck. The biggest badass in the world can go down to bad luck.
Well, for one, we now have the question of "if both are hard workers, and hard work is the only relevant factor, how can one beat the other?"
Then we have to consider numbers: Let's say only one in a thousand people is actually working hard. That's .1%. For Naruto, assuming all other countries have about half the population of Konoha, that'd mean there are 240
literal demigods walking the face of that world. We don't see that. We see two. To say nothing about someone like Rock Lee, who by that logic should be able to 1v1 Naruto and have a reasonable chance to come out on top.
This gets worse when we look at older villains instead of rival characters. Naruto we can
maybe give a pass on this one, because Shadow Clones, but for people like Deku or Asta? They are up against people who had trained as much as they have
before they were even born. This train of logic cannot sustain at that point, because the MC would quite literally not have been alive for long enough to match the more experienced opposition. He cannot put in effort if he wasn't alive to do so, after all.
Bad luck, of course, is a more logical factor. Plot armor is a term for a reason, after all. Issue now comes from a different narrative standpoint. Namely: How long can we keep pushing the MC's luck before it starts to become noticeable? After all, if hard work is all that matters, and both sides work hard, then that means the MC has to
always rely on luck to pull through. The first couple times? That's fair. However, the more you do it, the less reasonable it becomes.
For the audience to be invested, you need to be able to convince them of the fact that you're not cheating on the MC's behalf.
You are, obviously, but that's what suspension of disbelief is for.
Allowing for a meaningful advantage in combat, of course, circumvents that. You still need to break SoD once, when the advantage is introduced (i.e.: Man, sure is convenient All Might happened to be there right when Deku needed him, huh?), but you're mostly home free past that point, because the audience has accepted the premise of "the MC got lucky enough to be handed this gift".
