Seems like fan fiction to me, probably written after the trilogy was out, or at least after the second movie was out. The dialogue is very high quality for fan fiction (although Niobe's "what if they toughen the Matrix code" is notably bad, Smith's dialogue seems very plain, and Agents use too many contractions), although some feels slightly too rough or cornball, particularly Neo's. It couldn't have been a script written by the brothers after the first movie, because no mention of anything from it was ever made afterwards. It could possibly be a professional effort to come up with a money-making fourth movie, I suppose, but given the pretty clear stance of the brothers that they were through with Matrix movies after the trilogy, that seems unlikely. And there are a few typos, like "MORPHUES."
It particularly seems like fan fiction because it tries to explain/include as much as possible: Choi and Dujour as operatives, detailed attempts at explaining how Matrix code, Neos, Metacortex, and other mechanisms work, and so forth. It does these things fairly well, but this is intense fan stuff that wouldn't make for an interesting broad market movie.
I don't think any sane screenwriter would have written the "Gregory" character for Keanu Reeves. ;) And the non-dialogue in the script is far wordier, and less punchy, than the rapid descriptions in the Wachowski scripts.
There are also things that just don't seem to fit very well with the established rules and scale in the films: the missile-packing ring of ships in airspace above Zion, the unawakened but very powerful Gregory, the way Agent Brown addresses the cop, Neo's disintegration of the Metacortex building, Choi's last stand, Trinity's self-healing, Razor and Morpheus defeating Smith, and so on. I thought the mention that the Machines breed humans only by cloning was odd, and, in my view, an incorrect interpretation of how the pod system and fields work.
Similarly, Metacortex being a sort of physical Achilles heel of the Matrix feels like a lowbrow interpretation of what I think were for the Wachowskis much higher level abstractions; I encountered MXO players, for instance, who thought that the thing for Zion or EPN to do was to invade the Government Building, and I always found that to be a silly thing to want to do: okay, you took over a simulated building. Congrats. For the Wachowskis, the existence of the Matrix hinged on a complex and significantly abstract process of human belief and Machine desires, not on knocking down a building.
It goes against two major themes of the movies:
1) The whole plot of the Machines turning to an anti-Neo to counter Neo is just not in tune with the rest of the trilogy, which is about Machine (who is really Man, but denies it) vs Man, not Machine needing Man to go vs Man.
2) Morpheus wanting to destroy the Matrix and kill everyone in it is not in tune with his intense desire, in the movies, to save people.
So yeah I think it's fan fiction, but an entertaining read. I liked Morpheus' "reload me."