You've picked bizarre examples here.
Reliability isn't really about having weaknesses, it's not about saying "Oh, he's just like me and doing what I'd do". It's about creating an interesting and consistent character-- It's about understanding why they'd do what they do, even if it's not what you'd do.
Re: Weaknesses and deus ex machina... That's all superheroes. That's practically all fictional characters. First of all, Kryptonite is far from the only thing that can beat Superman. Many, many supervillains (and heroes), including random villain of the week types, have gone toe-to-toe with him over the decades and come out on top, or nearly so. Whether using weapons, traps, or their fists. It happens... exactly the same as every other hero. Hell, he was once beaten to death. "But he came back to life!" you say? Well, so have many, maaanny other superheroes. Also, how is Wolverine's "I can heal from anything in seconds and practically live forever" somehow MORE relatable? Or Iron Man's intellect? Batman's brain and skills and background? Any of it?
And before you or anyone else says "But, even then, you always know Superman's going to win in the end!"... Are you really sitting there with stories about Batman, Spidey, Iron man, Wolverine, James Bond or Sherlock Holmes, Captain Kirk or Luke Skywalker, or John McClane (the ultimate every man, for many) and thinking "Oh wow, I think he's actually going to lose and die, and the Earth's going to blow up, and that'll be the end of the series"?!
Superman has the DP Clark Kent persona-- That's "relatable" in the sense that you and others espouse is so important. That's the side that has to behave like an invisible coward (compared to Supes), is lovesick for Lois and pines for her, is occasionally seen as an easy target by Lombard and others, needs to do his job or get chewed out by his boss etc. And even as the ultra-powerful Silver Age or All-Star Supes, THAT side of him grapples with complex emotional issues, to-- How to best go about saving the world, wondering about Krypton and the parents he never knew, dealing the problems he has so far failed with (restoring Kandor, rehabilitating Luthor) etc. Yet... even through all that... Even though he may question how to go about certain things sometimes... He absolutely believes in the fundamental good of himself and most everyone else.
Honestly, more than any other (mistakenly) perceived lack of physical weaknesses... I think that's what a lot of the characters critic's have a problem with-- That he's more moral, he's kinder and he's better than we'll ever be (even though he does get angry and sad on occasion). But that's what he always should be. That's just one of the core reasons he's always been and always will be such a brilliant character... He's someone to aspire to.
All the most successful, acclaimed versions of the character over his near 80 year history of being one of the biggest fictional icons in the world ("Oh, people just don't like him" my ass) are the ones that EMBRACE all that with open arms-- From George Reeves to Chris Reeve, Silver and Bronze Age Supes, All-Star and Secret Identity, Kingdom Come and Red Son (stories about him reaffirming that side of himself)... They're all kind to a fault, all unapologetically good either all the way through or by the end.
Those that aren't on board with that, who don't get it and try to change him, muddy him up, have him brood... Well, you end up with what we're getting right damn now-- a disappointment.