Being connected to the matrix after being disconnected to the matrix just doesn’t make sense.
Using what means? The plug is removed from the back of his head and yet he can still access matrix code? That’s magic.
The only satisfying way to end the trilogy would have been to have the “real world” be some kind of sub matrix. Instead they made some kind of dumb super heavy handed Jesus analogy.
That would have been such a fucking cop out corny "oh look the real world is another matrix" nonsense like the movie 13th floor.
It's funny reading your posts because this is what I always thought about when people say they hated the sequels- Most were either too young and didn't click with all the philosophy 101, or they didn't pay attention and actually nitpicked shit they missed, but that were fully explained in the movies.
**When Neo reaches the source (when he speaks to the architect) he is then given the opportunity to reset the Matrix. He has this power now, we're assuming he has the code necessary to reset the Matrix already in him since the architect explains that was always his function, therefore after he reaches the source he is in tune with the 'consciousness' of all the machines in the real world. He even says this line "something is different, I can feel them" as in he can feel the sentinels coming. If we're going to get stupid with this we can say that yes he has a wifi connection to them and so can simply shut them off. You can decide to like this explanation or not that's your choice but it was fully explained in the film, and was not just "magic" .
***Interesting side note other people don't like or didn't fully understand: The point of the little girl in the train station is reflected in a few smaller scenes towards the end of revolution. When Neo is heading towards the Deus Ex, you see tiny machine like creatures approach him in a very 'awe' like manner. They know who he is, and in many ways are admiring his presence. Why? Well, what is hinted at is that he's closer to being both machine/man than they have been able to achieve in the past. This is further exemplified by the Oracle's last conversation with the architect that she played a dangerous game, but the game did produce the little girl both capable of being machine and of "loving" yada yada yada corny stuff either you care about or don't. But the Wachowskis definitely did wonders with this story and connected so many different aspects of religion, technology, A.I/machine learning, etc that would not be talked about in the mainstream media/culture for at least another decade.
EDIT: You know after watching all three movies in the last day (it's a holiday here today and it's raining so shut up) I think the biggest issue with Reloaded/Revolution is that they crammed too much action in between long winded expositions. The pacing was off, where as the original Matrix was almost perfect in it's action/dialogue balance. This turned off a lot of people that couldn't connect with the philosophical underpinnings of the movie. That disconnect made everything else meaningless, and most of what the Wachowskis do is very broad message driven, and not very character based. So if you lose that connection you're just going to occasionally watch some cool action scenes and then doze off in between.