For the most part, the sequels work or didn't work based on how much you were willing to buy into their universe. The first movie was a smash success because it did all the things you mentioned but every bit as importantly, it also was accessible in very specific ways. The entire movie was playing on this divide between our reality and the fiction of the movie. Its references and dialogue and structure all linked itself very much to things anyone can understand(e.g. feeling alone in the world, having a shit job you don't like, staying up too late, eating noodles...etc.) just regular real-life sorta stuff that kept any viewer gently engaged. In other words, it wasn't a movie that didn't give a fuck if the audience could keep up. It was a movie that gently coaxed the audience along with it at every turn. While simultaneously being an innovative action blockbuster.

The sequels, by contrast, go full-on into their universe. They say 'okay, now that we've established the fundamentals, let's geek out'. They literally threw out almost every tangible reference to our reality and stopped calling back to things we could easily relate to. That in and of itself is inherently polarizing. If you're interested, there's a lot going on. If you're not interested, it's a movie that (as to the title of this thread) doesn't really give a fuck at trying to hold your hand through it.

For me, Reloaded works as a deconstruction of the superhero. What you're dismissing as 'in there for the sake of...' content, I look at as integral to the basic premise where it's not about what those conversations were(though they're not totally irrelevant either) about it as much as it was simply about having them. The first Matrix movie ends in a very simple and cinematic fashion. Neo, literally a superman, flies off to (ostensibly) save the day. The second movie says "... except power on its own isn't an ends" and follows Neo as he meets a dozen new voices who all have a different opinion on what he's supposed to do with the payoff in the end summing up (quite bluntly) as "The problem is choice" and specifically underlining our unique capacity to make choices that are counterintuitive or against our self interests for reasons that don't make any logical sense. That, when spun back around onto what superheroes are and what they represent, is a cool concept. Realistically, Superman 'should' be more like Doctor Manhattan, Superman being morally righteous is a decision he makes, even if it doesn't exactly make sense for him. Which, I know isn't the headiest stuff in the world, but it was somewhat ahead of its time and we didn't really see these sorts of questions and problems discussed in superhero movies much until MCU 2.

Anyway, about Neo and "Magical powers" in the real world. He really didn't have the same powers he had in the matrix though. He could blow up sentinels and 'see' Agent Smith/Machines but that was basically it. Considering sentinels are already established to have a wireless link to the matrix, it's a very small leap to figure Neo(whose entire body is full of machine interfacing hardware) might have one as well, not enough to jack-in with, but enough to send an 'explode' command to sentinels. Again, we're talking about movies that don't hold the audience's hand through everything. The specific mechanics of how that works don't need to be explained verbatim.