The Matrix is actually an interesting thing if I recall correctly.

The Wachowskis really wanted to tell a huge story, they had so many ideas and multiple sequels across many mediums.

They had funding issues, or there was little confidence the film would be a success, so the very ending of the first Matrix is just sorta tacked on.

Neo in the phone booth telling the machines he's about to change everything as he just flys away, completely breaking their reality. It's a "and they all lived happily ever after" ending.

Of course The Matrix was then hugely successful.

So now the Wachowskis get to tell the story they intend, hell they get to do pretty much whatever they want.

As a result Neo is weirdly much less of a badass (but still badass) as he sort of finds himself during the events of Matrix Reloaded.

But if course I bring this all up because the Wachowskis did get to make all the things they wanted. Reloaded & Revolutions were at least part of the story. The Animatrix and other shorts, part of the story. The multimedia continuation of the story where you could jump into a video game to see part of the story, or into a an MMO and live in the Matrix.

The Matrix was always envisioned as this huge thing. It just turned out that having the idea and executing on that idea is hard. The films didn't quite live up to expectations (still good mind you, but a step down). Part of the films "missing" with the idea that it would be something you can experience in a video game. The story continuing on in an MMO that took a while to launch and then had major issues.

Which is all to say sometimes even with good intentions and ideas, it's just difficult to get an idea perfectly onto screen.