They're making a Matrix 5.

[Vahnavoi]

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The idea that there is another layer of control is a pretty small and obvious thing. Yes, yes of course the enemies have another plan for evil. The mere existence of a sequel guarantees that. So? What is the story told by it and the opposition to it?

Why are you asking? These aren't unanswered questions in context of Reloaded and Revolutions. The original asks if Neo is the promised hero in the war of man against machine - he is! Animatrix shows that the conflict might have more facets to it - maybe men are less innocent than thought and maybe machines can have sympathetic reasons for what they do. Reloaded reveals the promise of a hero is a set-up - this has all happened before and Neo cannot live up to the promise simply by playing the part laid out for him. Revolutions is all about Neo's reaction to this and whether he can live up to the faith placed on him and redeem the concept of the promised hero - which he does by negotiating peace with the machines, becoming a champion for both sides of the war.

The movies aren't subtle about this. Being critical of delivery is no excuse to miss the story before your eyes.

As for the discussion of philosophy, it isn't a unique concept, but is at least as old as Plato's cave. Discussion of simulation and unreality is very, very old, and a reference to a specific book doesn't make the concept any more novel. It's a fine basis for the story, sure. It is not the story itself. The first movie would be empty without the story of Neo. The sequels fail to replicate that story. More philosophy references are merely setting details. They are not story.

Firstly, both the original and the sequels are perfectly aware of the philosophical traditions they're part of, containing obvious references to Plato's cave, gnostic idealism and their equivalents in Eastern Philosophy. Second, in cinematography, there is a distinction between plot and story. "Plot" is the sequence of events, the what, when and how, while "story" is the themes, characterization and emotional reactions, the who, why and feel.

The philosophical discussion with the Architecht? That's story, tons of it, right there. It's all about Neo's character and how he reacts to the revelation before him, with myriad reflections on the Architecht's screens literally showing you alternative ways the story could play out before zooming in on the specific one the movie wants to focus on.

You can dislike the scene all you want but if you think that discussion isn't or doesn't have a story to it, you are just wrong.