I do agree that if your whole thing is wanting normal people as protagonists with an actually-too-powerful-to-defeat villain, then powering up the protagonists sort of undermines what's interesting about that story.
But normal people outsmarting overpowered folks is a staple of stories -- myths and faerie tales especially! Characters who could never defeat this guy have to figure out how to set him up to orchestrate his own failure, or exploit his personality flaws to lure him into a trap -- or, their own empathy and willingness to sacrifice leads them to act in ways he didn't plan for, because that sort of behaviour doesn't make sense to him.
A very simple example of the first kind that springs to mind is Aladdin vs. Jafar in the Disney movie. Jafar can do literally anything and Aladdin is Just A Guy, so the only way he can possibly stop Jafar is to trick him into undoing himself.
It's a children's movie, so Aladdin's "haha im not impressed" routine is pretty obviously telegraphed, but it's not a bad move -- Aladdin knows something about genies that Jafar doesn't, and uses that knowledge to trick him.
I think this is kinda a matter of, while you're writing, you wanna look at what you have the heroes planning and ask yourself if your bad guy should know better. Is this something he should've planned for? Something he should've seen coming? And then you work with that -- what precautions would he have in place, and could the heroes work around them or plan for them? Or is there a reason he didn't or couldn't have those precautions?
Another thing to ponder is that if there's a weakness that can be exploited, but the heroes have to work for it, it usually doesn't feel cheap. Like, almost nobody yells about how dumb an exposed ventilation shaft is when they first watch Star Wars -- because Luke had to work for it, because that scene is challenging and stressful, and so it doesn't feel unearned or cheap when he exploits that flaw.
