The biggest problem I had with it is that the bullet-time trick was used too much this time. It also didn't slide into and out of these bullet-time sequences nearly as smoothly as in the original. It was as if they had decided, "Okay, here's another place we can use bullet-time." In some cases, it was okay, like the jumping on to and off of cars on the freeway scene.
The second problem I had with the movie was they tried desperately hard to make it sound intelligent. The screen-writers must have had sore fingers after all the thesauruses they went through. And everything was thrown at you so rapidly, you are bound to miss something, and/or get confused. Actually, this was probably done in order to get you to come watch it again to try to puzzle it together; or give you time to look up some of the words. Even I almost lost it for a second. (This isn't saying I necessarily understood everything and can explain it, as I'm sure that there is some twist of meaning which will show up in the third movie that I haven't thought of.)
The third thing which I found troublesome was length of the fight between Neo and the multiple Agent Smiths. I know that they are trying to top the impressiveness of the original Neo vs Smith fight in the first movie, but even that one had a break in the middle.
So, other than these things, I must say they came up with some cool ideas. They expounded on the glitches of the matrix. In the first movie, we find out why you experience deja vue (I'm not going to use tildes, so get over it), now we find out about stories of ghosts and vampires and UFOs. We even found out that a silver bullet can kill a program... I wonder if that would work on the agents, or have they been "upgraded" too far? ;)
Now we also start delving into the realm of what is real, and what really is real.
Is Zion, indeed, part of the matrix? Is the matrix part of Zion, perhaps?
We need machines in order to survive. Shutting them off turns off our water and air recycling, our heat, our light. Shutting them off kills us.
The machines need people in order to survive. A living being is grown in a pod and the energy given off powers the machine. Killing the people shuts off the machines.
The parallel nature here is obvious, and is meant to be a part of the story and the destruction of one or the other, or both, is supposedly meant to bring a reaction and be thought provoking. Hopefully, it doesn't turn out to be predictable like much of this movie did.