A huge problem is that most people can't handle the ending of the Movies... If three had a more... "average movie-goer" ending (NEO WINSSSS HUMANS ARE FREEEE!!!!11!), then more people would have liked two, IMO.
The first movie put you in a world that you'd never dreamed of, storytelling wise. The second shattered all of that. People who aren't fans of the movie just can't handle that. A lot of non-fans still don't understand Neo's sacrifice was for man and program alike. In fact, in general there's a lot they don't understand.
That's kind of why the W Bros stepped in the way they did at the end of PON. But we already know all of this...
As to the OP, is it the end? Probably. I don't particularly see the W Bros releasing the rights so that some other directors/writers could take a crack at a movie, and no game company is going to make another game after the disasters that happened before. Don't forget, MxO wasn't just received poorly, so was Enter the Matrix and Path of Neo.
Sucks, but I think this might be the end of the rabbit hole.