What a sad ending!!!! So Many questions, plot holes, remain!

Rating: Null/10 (10 November 2003)

After we were about 2/3 of the way into this movie, my wife and I were thinking that the critics had watched a different movie. Then the ending came and I realized what everyone (who did not like this movie) was referencing. There are so many un-answered questions!
The first is...
Can this really be the ending of the series, or are the brothers Wachowski going to surprise us with a part four? If so then than I can recall all of this review and wait for the "Real" ending. If not, then the questions remain...(all indications point to this being the last one).
WARNING "MAJOR SPOILERS"...
Second question...
The first major plot hole. If no one has ever made it into machine city (where all human plugged into the Matrix are kept) then how the hell did they get Neo out (and into the Nebuchadnezzar) in the first movie? And for that matter how did they get the others (Morpheus, et al) out before him?
Third question...
Making peace with the Matrix does not achieve the main goal of freedom for humans (which Morpheus spells out in the first movie). All Neo achieves is that he stopped Agent Smith. Humans are still "trapped" in the Matrix! What happened to Neo?
Fourth question...
In the first movie, Trinity says the only defense against the Sentinels is the EMP. She must have known about the Guns in Zion, right? What about those on the ships? Why didn't they have an EMP installed in the Dock at Zion?
Fifth question...
Morpheus talked about the Agents being programs, which have to obey laws and have limitations. "...yet their strength and their speed are still based in a world that is built on rules. Because of that, they will never be as strong or as fast as you can be." How then does Agent Smith become such a nemesis for Neo?
I really like this movie up to ending, and then everything we learned from the first and second movies begins to mean nothing. Everything humans are fighting for is undermined by the ending. What a sad way for a great trilogy to end!