Just watched the whole trilogy over the past week, and though I'm pretty intimately familiar with the first movie, it's been well over a decade since I'd seen the sequels, so I'd thoroughly forgotten everything apart from the general pop-culture awareness things. My general takeaway is that the sequels weren't as bad as people made them out to be, but they definitely don't follow on in the same direction that seems to be set up at the end of the first movie, and they seem to be actively trying to prevent you from understanding the cool ideas within them.
The primary example for this is the scene with the Architect, in which Neo learns that the prophecy of The One was made up by the machines as a way to corral the freed humans and make them easier to control. This is a really interesting concept, and could totally be explored in greater depth, but the actual on-screen explanation of this is a dude in a chair speaking in deliberately difficult to understand phrasing (concordantly, vis-a-vis, ergo), and no follow up. Compare this to the scene in The Matrix where Morpheus takes Neo through his 3D slideshow presentation of what the matrix is, the history of the machines, how the world got how it is, and it's clear that there's a real lack of 'show, don't tell' in the sequels. There's no visual interest to aid the exposition, and there's no time dedicated to exploring the concepts presented. It's as if the movie doesn't want you to know that it has cool ideas.
To make matters worse, what Reloaded does decide to spend time on is an extensive and unnecessary rave in a cave scene, an extensive and unnecessary orgasm-inducing cake, and several extensive and unnecessary fight scenes in which one or more those involved is trying to just leave, and could do so at any moment, but instead decides to hang about so the scene can be more spectacular. Don't get me wrong, I'm all for action spectacle, but without justified motivation, the action scenes feel overly indulgent.
You may have noticed that this criticism has so far been centered on Reloaded and not Revolutions, and that's because I think that any of the problems that Revolutions has are all inherited from Reloaded, and the new content it introduces is all executed about as well as could be hoped for. All the effects of the Zion battle sequence hold up surprisingly well despite the age of the film, and after the first act (up until Neo gets back into the real world, all of which feels like story beats that really should have been part of Reloaded but were moved over into Revolutions so as to make the movies more sensible lengths), all the plot beats are well paced and keep escalating towards the conclusion.
In summary: The Matrix sequels have a lot more going for them than people give them credit for, the reason behind the negative reception isn't due to the movies not having an interesting story to tell, but due to them hiding this interesting story behind layers of unnecessary self-indulgent scenes and a lack of effort to communicate or explore the cool ideas when presented.
Then again, maybe I'm just bringing too much of my own concrete