The character didn't even feel like Agent Smith, either. It lacked his edge...he was always the most hostile of the agents, a group particularly given to lack of empathy and chill, so to suddenly throw a different actor at us with wholly different motivations and attitude is to basically just use a wholly different character altogether.
The whole end fight scene was repetitive and boring, and the movie basically goes full mask off and talks about how executives just want a cash grab early on. It manages to be both wildly incoherent as a film and also still boring. Elements like using people as weapons was discussed a bit in the first film, and while it seems as if they wanted to use that idea in this film, they didn't really bring any deeper insights to it.
Yes, of course their philosophy is awful, but that doesn't mean that the audience should be bored out of their mind. The audience loves to truly hate a villain. Agent Smith we love to hate. The Architect just makes us think about getting KFC instead of watching to the end.
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?
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.