My opinion of how the series went after the first one: bleh.

Reloaded was crap because all it did was move from setpiece to setpiece. It showed us all of these assorted events that happened in chronological order for the sole purpose of advancing the whole saga or whatever you want to call it--at the expense of making one cohesive movie.

Revolutions did the same thing but to a lesser extent, and it was way too much a hybrid of Star Wars and LOTR for me to really care what was going on. Niobe and Morpheus are Han Solo and Obi Wan; Neo (in the real world) and Trinity are Frodo and Sam; Neo (in the Matrix) and Smith are Luke Skywalker and Darth Vader.

The only difference is that we get spewed this nosensical wannabe intellectual psychobabble so that people who are not as intelligent as they think they are get to play philosopher with possibilities that exist within the overall universe created by the three movies plus the extra bits of the Animatrix and the video game if someone really has that much time on their hands.

Another issue I had was that the society inside the Matrix in the first movie was actually sort of like real society. In the second two movies with all this stylized clubbishness nonsense that goes on it got out of whack yet again. The Matrix is supposed to approximate real life and the Marovingian (however you spell his damn name) still exists within the Matrix and so does his club so you would think the people there would at least try to resemble what the Matrix was trying to mimic.

I will say however that the one scene in the train station was at least indicative of how cool the series could have been.

I'm sorry but I'm not going to spend that much time on a franchise that at its core was able to produce only one truly good movie.
That was explained in Reloaded. They plug into the gate control program the same way Neo plugs into the training programs in the first movie. It's a separate program outside of the Matrix.