I'm glad to see some positive reflections on the sequels, OP. Maybe I'm just a Wachowski apologist, or maybe I was so young when I saw the sequels that my perspective is skewed. I don't really care either way.
I think the Wachowski's definitely knew what they were trying to say. When I was a teenager, the sequels were always the films I constantly went back to to try and "figure out". To others, maybe it was bad storytelling... but to me it was fascinating. I feel like I've got a pretty good grip on them now, and that's pretty gratifying.
The Wachowski's said something similar around the release of Cloud Atlas, but I think the following adequately sums up the sequels thematically: the idea of reality ought to be defined subjectively, rather than objectively. It doesn't matter which reality is "objectively true". Your reality is defined by the things that mean something to you. Neo begins with the search for objective truth... in what lies "beyond"... but he ends up anchoring his idea of reality in humanity, and more specifically in Trinity.
The architect's speech is so intentionally disorienting (meta, even), but the point is clear. The rabbit hole goes deeper, and the system of control doesn't end with the matrix. There's something more going on beyond Zion, the machines, and the agents. This is made clearer at the end of the second film when Neo is able to use his powers in "the real world". How deep is Neo willing to follow the rabbit hole? I think at one point Neo simply says "Fuck this. This isn't the shit that matters to me." He chooses love over the system, and in so doing he defines his own reality. He makes that choice the second he chooses to walk out on the architect. It's basically just existentialism 101.
In some ways, that idea is in direct contrast to the first film... but in other ways, the original basically begged the question. What if our world isn't real? Turns out it isn't... but can't you ask the same thing about the next layer of "real" you find yourself in? I think that's an important factor in tracking Neo's growth as a character. The whole trilogy is basically a search for meaning. Neo begins by searching for a reality beyond the one pulled in front of our eyes. He searches for it in computers, and in the beyond. He's convinced there's something more out there. In the first film, he finds it. In the sequels, doubt grows. How "real" is the real world? The architect gives us a scenario resembling an infinite regress. A system of multiple layers of reality, and repeating cycles...all designed to assert control. That entire sequence is basically a continuation of Neo's discussion with Morpheus.. only colder, more complex, and less human. He's literally talking to a computer, and what's his reaction? He flips the bird, says fuck you, and goes off to save his girlfriend.
Neo chooses to reject the architect's machinations, and thus breaks the system. I think it's intentional that we never really have a clear idea of what exactly this "system" entailed. We're never sure why Neo could use his powers in the real world (outside of the notion that the real world was just another layer for those that rejected the Matrix), and why Zion was caught up in this meta-cycle of destruction and resurrection. Neo never fully knew either, because he no longer cared. He see's that he's just one of the system's many tools, and he chooses to walk away. In so doing, he chooses to define his own reality through the people that mean the most to him, rather than through increasingly obscured, objective notions of "the real". He's fighting for something he believes in now; something human. He's lost the existential edge he had in the first film, and his arc is complete. The Matrix Revolutions represents the consequences of Neo's choice played out in real time. I don't know. I think it's pretty powerful stuff. Maybe a little bit obscure, but that's what made the entire trilogy live on in my head. All three films are fairly obscure, at least at first glance.
I think they're vastly underrated sequels.. and they make up a great trilogy overall. I felt the same way about Reloaded and Revolutions as you do now when I was younger... but my opinion has swapped in recent years. Revolutions has better pacing but I find Reloaded is the more intriguing of the two. That said, I'd concede that the first film works the best as a single tale. The sequels aren't as successful neither in terms of storytelling, nor in the communication of their ideas... Still, I think there's so much to dig into and all three are very important to me.
Anyway... tl:dr: Cool movies. I might be over-reading them, but I'm totally fine with that.