It wasn't The Matrix in terms of VFX and world-building but I thought Duncan Jones' Source Code (2011) did a solid job of exploring that brain in a jar, alternate reality mind fuck shaped hole the Matrix left behind. And, even though it wasn't that good and kind of dragged Mr. Nobody was a pretty decent attempt and so was The Fountain (though that's more of a spiritual Tree of Life like movie than mind-bending sci-fi). To be honest, there's been quite a lot of original sci-fi since The Matrix came out - I know it's mentioned in the article as an anomaly but Cloud Atlas is a good example when it comes to world-building along with Vanilla Sky, Inception, and Looper to state just a few.

If the author means that there won't be more films exactly like the Matrix... then, yeah. No shit. Why would anybody want to see a bootleg copy of something that's already out there, isn't that why the Divergent series failed? I don't know, man, I'd say we're not too far of a golden of sci-fi; studios are more or less competing to give talented filmmakers (Villeneuve, Nolan, Jones, Scott, Cameron, Besson etc. etc.) huge budgets to develop original ideas that tend to do pretty well - and even if they don't (Blade Runner 2049) studios just class it as a write off and let the auteur get on with another project.

I massively disagree with this article, I know it might be hard to feel like there's original stuff out there but it doesn't take that long to find it - it might not be promoted half as much as an Avengers movie (which I would also argue should be classed as original, or at least semi-original, sci-fi) but it's out there, all you've got to do is look.