The problem is that beneath it all, the brothers are just not all that creative and nothing in this story is in any way original. The Oracle (if she is to be believed) thinks that the human/machine link is not one that can ever be broken. She's not helping Neo come to a place where he can destroy the matrix, free the people and blow up all the machines (that would be suicide on her part). She thinks that Neo will come to a realization (as the Counselor was helping him understand) that people can't live without machines and in their world vice-versa. Now, if the brothers were clever, they could explore all the gray areas of this dependancy... however, they're not, so what you're going to see in the next movie (and I'll eat my hat if I'm wrong on this) is that Smith, who is now a megalomaniacal dictator bent on domination in both the Matrix AND the real world will force Neo and The Donald Sutherland wanna' be Architect to join forces to do a Norton anti-virus sweep. Once that's accomplished, Neo will recognize how much of a machine he himself has become, Southerland's cheap replacement will realize how much humanity has to offer and we'll have a happy ending of the humans in the matrix being set free in exchange for helping build the machines an alternative power source (dogs perhaps?) or there might be the slightly more interesting twist that the humans will prefer to live in the matrix, under the condition that they all be made aware of the fact that this is the case, so that they have "control" over their destiny.
In any case, the brothers are too focused on having (completely non-sensical) fight scenes rather than explore complex alternatives to the most obvious (and frequently stupid) plot paths.
As I said before, if the machines' ultimate goal is to have a stable power supply that doesn't revolt and if the machines don't get anything out of the battle (which we keep getting told they do not) then the architect's obvious path is to not give Neo any options, to kill everyone in Zion and hope that the next anomoly doesn't have any help in the outside world. We have not been told what the Architect gains out of giving Neo the fantastic luxury of making any choices in the end game. It's just a gaping hole in the plot.
Another gaping hole... Why does Neo still "Fight" with the agents/vampires/ANYONE?! We've been shown that he sees THROGH the code, he should be able to simply walk away from any code entity or completely corrupt them with the touch of his finger. I realize that the girls wanna see Keannu kick ass, but then they shouldn't make him into a God in the first movie if they want to use him in more fight scenes... save that for the ending.
OH, and I hope that in the final episode we get to see more sweaty hippies raving for 15... no 45 minutes. Yeah... that was great... gimme more slow motions sweaty cave raving... UGH. ok, enough for now, I'm beginning to sound like I didn't like the movie... when in fact, I liked it quite a bit (my standards are SO low).
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