I don't think it's "beyond you", I think it's so simple you passed right above it.

A "philosophical super-hero" in the context of Matrix, circa 1999 is something along the lines of:

Everybody's asleep like Jim Careys in the Truman Show. Reality is not what we think it is. We're all slaves, we're all miserable even if we think we're happy. It's all a lie. “They” control us. “They” know and keep us ignorant. “They” are the reason why we suffer so much and we're not even fully aware of it.

Enters Neo. Neo is a cool dude who should have been Will Smith but he declined to do Wild Wild West — crazy sci-fi in the machine seemed less blockbuster-worthy than big machines exploding in the Far West, yeah, that was a bad call. But I digress.

Neo who's not black, unlike Morpheus, is not like the rest of us. No no no: he's AWAKE(ning). He's woke, man! Like F, this should have been Will Smith, that smug look haha. Oh boy, I digress. Not that Matrix itself is boring but.

Then there's Zion. It's really the Bob Marley ideal, because why not, heaven can only be full of hippies of sorts, and the idea is that if humans "escape" the bad guys, they can all go party to Zion. Cue NOT Laureen Hill, that was a fail honestly.

So, imparted with this supreme Knowledge about “them” and heaven and Morpheus' BFF and so on, Neo can do a whole lot of cool tricks because he now "knows". And there he goes, solves the puzzle in a trilogy because that sounds nice, and the good people are now free. Probably. Or not. Who cares at that point. The whole story was never about that anyway.

So, that's the level-1 "philosophical hero". He just "gets it" and that makes him stronger. There's also a big nod to human versus machine in that the Matrix, the bad guy-s, they don't understand "love" the way we do, and Neo.. well, he's the romantic you know, he loves Trinity and that's the key to his ultimate surviving. “A truly original take on what it means to be human”, said nobody ever who wasn't born the day before.

So, yeah, I'm sure you can see all of that, and (rightfully imho) thought it wasn't much "philosophy" material.

HOWEVER! there's level-2. For the "woke" people among us, you know, those who "get it" like Neo. (I'm joking but I think it's a little bit like that, there's a smugness to Matrix fans, even those who seem to indeed "get it".)

This is my liberal interpretation of level-2. I've looked at YouTube videos analyzing the movies because frankly I didn't get it, like you. And then I had my own "awakening" in life, but it's much less glamorous than Neo, it means shitty experiences for stupidly long times and then somehow emerging the other side and being alive enough to tell about it. Long story short, I kinda "get" what they possibly mean. It's as old as the oldest mythologies conceptually, e.g. the "Maya" in Hindu (Sanskrit: “magic” or “illusion”).

So the matrix is an image for "whatever you think is impossible", the opposite of what is sometimes termed "abundance" mindset — I can't do this, I'll never have that, this is impossible for me, etc. It's a veil on reality, and critically self-imposed, of our own doing in a modern interpretation, more agnostic about gods if you will.

Anybody who does something in this world must at some point on the way remove such limiting thoughts, usually much wider than the mere topic — whether business owner, moviemaker, musician, scientist, etc. In HN of all places the sample is skewed as hell, but some of us probably see that most people are self-imposedly very limited in their "possibles".

I could elaborate but you get the gist. Everything else is filling with analogies and good moviemaking, probably, or not, whatever, who cares at this point.

Level-3 exists, some people do that: they take pop content and slap philosophical references because "quotes" and "easter egg". But then they elevate the easter above the egg and we're all dying of an empty brain because Matrix is now officially better than the Odyssey and La Comédie humaine combined.

Did any of this speak to you, should you have read even just 1 paragraph? :D