OK, I don't understand these criticisms of the plot. In many, many ways, the plot was developed well past what was exposed in the first movie. By comparison, this was a philosophical masterpiece, and the first movie was simply another "Rambo" movie. Yes, I loved the first, but I am astounded that anyone can call this a dissapointment.
A few comments to think about:
This is the sixth iteration of Neo. His personality is an enevitable result of the code of the Matrix... something (a glitch) they haven't been able to get rid of without disrupting all the nice things about the current Matrix. What does that mean? If his personality is a recurring part of the code, then his persona, intellect, and abilities are not a result of his human mind. Indeed, it seems as if the whole of his conciousness as a human has in a very real way been overwritten by the Matrix program. Whereas other humans in the Matrix develop their personalities as a result of their genetics and life experiences, Neo seems to be the result of Matrix programming and life experiences. A very important distinction. Just as the agents, twins, and the Oracle are parts of the Matrix code, so is Neo, at least in part. How was he able to stop the machines in the "real world" at the end of the movie? Well, I'm not sure precisely what route they will take with the plot, but to venture a guess it could simply be that the Matrix monitors all parts of code that make up the Matrix, and the machines can monitor Neo in the real world in some way, since his psychology is a product of their programming.
About the twins... that seemed pretty obvious. In the first Matrix, we only knew that there were humans plugged in, and agents that were the "police force" code of the Matrix. We also knew about the Oracle, but didn't know "what" she was. At the time, it seemed innocent enough to think of her as a human with gifts... just like Neo. How wrong we were, on both accounts. In the second movie we were shown that the Matrix is much more complex than we had believed. There are parts of code that malfunction, or even rebel. The twins are such an example of code that doesn't "go along with" the normal operation of the Matrix. Several characters are as greedy as any humans... and I think that is very important philosophically. We were shown that all aspects of humanity (except compassion... haven't seen that one yet, except perhaps in Neo) are represented in the machine world. And the discussion in Zion about the machines that they rely on to stay alive (mechanical ventilation and such), man, what a strong message. The war between man and machines was began simply because man couldn't find a way to coexist. It was man's arrogance that led to the Matrix, and I'm interested to find out how in the third movie man's arrogance can be overcome to disband the Matrix.
On Neo's choice... what a tough decision. The "rebellion" had occured five times already, with the end result of Neo going to see the Architect (by instruction of the Oracle, who is as self serving as most other characters in the machine world). The choice is to either cooperate, allow the rebellion to be crushed, save for a few who will seed the new Zion for the next iteration, and the human race lives; or, not cooperate, destroy the core programming as was his intent, and allow both Zion to be destroyed as well as all humans all humans connected to the Matrix - the human race dies.
Best I can tell, Neo made a third choice not anticipated or planned for... he simply did neither, and left the Architect and the Matrix intact. In a way, it seems he postponed his decision, which might be the road to true freedom from the Matrix. I think the machines had planned for one or the other options being chosen. The first five times it was the easy option. Had it been the other, I think the machines would actually have kept a few humans alive, to rebuild the Matrix after suffering enormous machine casualties and setbacks due to the scrambling of the core programming by Neo, and the loss of their most important energy source. But comments made by the Architect, about "acceptable losses," leads me to believe that that option had been planned for by the machines, and in reality either option would have been fine with them... either one assured their continued dominance of the planet. Apparently, the third movie will be the exploration and revelation of how that third option plays out. Perhaps they take the fight somewhere they machines didn't expect and didn't plan for... the real world. Perhaps they never realized that Neo being a product of the Matrix means he has some control over machines in the real world, just as the machines have control over humans in the Matrix.
Who knows... it will be interesting. But a dissapointment, or devoid of plot development? Man... what more could you possible ask for? It's a philosophical tour de force. Maybe a bit overdone on the action scenes, and with a couple of cheesy "geek porno" scenes thrown in, but all in all it's a much better sequel than I had thought possible.