The second and third movies of the Matrix trilogy are something that people just love to hate. It seems to be some kind of universal consensus that these two movies outright suck, and anybody who doesn't think so is just plain weird.
Yes, I have encountered this kind of attitude in real life (and of course online). An attitude like it's incomprehensible how I can like the Matrix sequels.
I think that many people who diss the sequels don't really get their point, and they would actually start liking them if they gave them a second chance and tried to understand them. Let me write about my theory of why the sequels are so universally considered so bad:
The first Matrix movie was something new and exciting, and was universally considered cool. It was one of the few movies of the period which really stimulated people's imaginations.
In a way, the first Movie was perhaps too innovative and too popular. People started forming their own version of the "Matrix universe", forming their own theories and their own histories of how things happened and how the story could continue in even more cool and awesome ways. People discussed these theories and speculations online, and many such ideas got popularity.
Rather inevitably, the Wachowski brothers had their own vision of how the universe of the Matrix worked, what was the history of this universe and how things would continue, and their version was inevitably different from fan expectations.
The Wachowski brothers had the entire trilogy drafted out from the very start. The script for the first movie was slightly modified to make the movie slightly more independent in case the movie would flop and no sequels would be produced (I think there was quite some executive meddling in this whole process). However, it was still basically the first movie of a trilogy all along, and the entire story had been drafted from early on.
But of course the continuation of the story was, rather inevitably, quite different from what fans had theoretized and speculated after the first movie had been published. Thus when the first sequel came out, fans got a feeling of "they changed it, now it sucks", even though they didn't change anything (it was simply different than what fans had imagined, that's all). This is one of the major reasons why it got such a huge backlash.
Another affecting factor was that the first movie was, buntly put, a dumbed-down version of what the Wachowski brothers had originally planned, mostly due to executive meddling. In this case the executives were actually mostly correct: The "dumbed-down" version was actually so good that the movie got immensely popular.
The problem with that was that this "dumbing down" was, probably inadvertedly, done at the cost of the sequels. When the first movie got immensely popular and the sequels were greenlighted, the Wachowski brothers had no need anymore to dumb down the story, and went more with their original vision.
For this reason the sequel was significantly more difficult to understand than the first movie, which was basically just mindless action. For example, I'm pretty sure that at least 90% of the viewers did not understand the Architect's speech at the end of the movie the first time they saw it. They heard a lot of words, and some of them had some vague meaning, but the overall concept of what he was talking about was completely beyond their heads. (Personally, I did not understand that speech at all the first time I saw the movie, so I can't blame anybody.)
Even to this day many people have the misconception that the Architect's speech was just some random technobabble which was a poor attempt at sounding cool but which had little substance. People think like this because they don't actually give the movie a second chance nor try to understand what's actually going on.
On the contrary, once one knows what's going on and what to expect, the Architect's speech starts being very comprehensible and illuminating, explaining an enormous amount of things in just a few minutes. You simply have to give it a chance.
(In fact, I have written an entire page on the subject.)
The second movie is actually full of references and hints about the history of the Matrix universe and how things work. You just have to know to look for them, and then you'll see them, and you'll realize that the movie is a lot deeper than it seemed at first.
The three movies in the trilogy are also quite different from each other because they are intended to be different. The first movie happens mostly inside the Matrix and deals with the awakening of Neo. The second movie happens about equally inside and outside, and is mostly about the history of the world. The third movie happens mostly outside the Matrix (most scenes inside are mostly irrelevant or not really related to the Matrix per se) and tells how this Neo succeeds in doing what the previous "Neos" couldn't, how the liberated humans actually don't lose the battle against the machines.
What fans wanted in the second movie was another first movie, just with more of the same, with perhaps some dumbed-down explanations of things. They didn't get what they wanted, and now many fans of the first movie are dissing the sequels without even giving them a second chance.
What they got was a rather different movie set in the same universe with the same characters, with hints of explanations which need some thought before they can be fully understood.
In my opinion these people are being dumbasses. They are completely missing the chance of enjoying two great movies with deep and involved storylines, usually simply because they didn't understand those storylines the first time. They wanted more of the same dumbed-down mindless action of the first movie.
Curiously, the same phenomenon happened at a smaller scale between the second and third movies: After the initial shock of the second movie being actually different from what fans expected, some of them actually embraced the second movie as an ok continuation (which got some popularity in itself). Then they, once again, formed their own theories and speculation, and waited anxiously for the third movie. And once again, the third movie was different from what they expected, they got disappointed, and they completely dissed the third movie. Once again, "they changed it, now it sucks" (even though they didn't change anything).
Once again, they were missing the point completely. The third movie wasn't even supposed to be another second movie. It was supposed to be different. And also the third one contains explanations (which are, in fact, even subtler and harder to get than in the second). These explanations are just not what the fans expected (and many of them didn't see any explanations at all, which was disappointing to them).
These people are missing the point and depriving themselves of two great movies just because they were "different" and they didn't fully understand them the first time because they were not dumbed down, like the first movie was. They should really give them a second chance.
(Not all hope is lost though. Some people have actually told me that they watched the sequels after reading explanations about them, including those I have written, and they actually liked the sequels more because of that. It's nice to know that at least some people are willing to give the movies a second chance.)