It was never a masterpiece despite some cool fighting scenes.
On the other hand it's no more silly than all those kindergarten dystopias the kids love these days: Hunger Games, Divergent and so on

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The aforementioned movies were groundbreaking in many ways, whereas this movie didn't do anything original in terms of visual effects and storytelling. So, not really a fair comparison.
That being said, the one effect in this movie that looks really unconvincing now, is Brandt's sliced face. In addition to that one, the movie sort of has that Syfy movie channel look. But overall, it's still a fine looking movie to me (and those gun fights are as impressive as ever).
Hey there, Johnny Boy, I hope you fry!

It looks a bit cheap, some of that early CGI is really noticeable by now, but it's still enjoyable, at least those gun plays.

The Matrix (not quite an original movie either - and you mentioned only sequels) has not aged that well, especially not the computer graphics they used.
Equilibrium in itself was a ripoff of other movies - so I'm not surprised that it showed its aged one year after it was made even.