Well 1st off IMO Neo should have taken a back seat in this movie, in the matrix he's a god no one can hurt or kill him. There's no suspense in any of his fights because he's like Superman if Kryptonite was non existent. Totally Immortal.
Now if it had been about Trinity and Morphues that would have been much better they can be hurt, die, held captive. When they get hit you think "Arrg! go on get up, keep fighting" they struggle for their life, Neo just seems to pass the time killing agents. BUT with the ever present Neo they cant die because with one whisper from any of them Neos God-sense is tingling and he flys round the world and pulls their fat out the fryer. <_<
If it was a "thinker" a bit like the last one, subtle hints about the nature of the Matrix as the Architect explains would have been given so we, our selves, could arrive at that conclusion thus making us think. Instead you have the God from the machine (Deus Ex Machina) syndrome of every thing going to shit and some divine presence coming in the final act (the architect being the "god", the creator of the matrix) and righting everything or in the case of this movie explaining every thing. This style of story telling is pretty pathetic and also insults the audience.
I also felt the scenes from inside Zion where not necessary,they where too Episode I & II for my liking, the political side and council where very Episode I the soppy shit with Neo and Trin was too Episode II in that tacked on romance kind of way.
Morpheos' "I have a dream.... we will fight them on the beaches .... there is no try" speech was delivered in such a half hearted manner.
The scene with the French guy in the restaurant was way to long, out of place, nonsense, self indulgent pseudo philosophy/psychology. Most of that would have hit the cutting room floor if I had any thing to do with it.
So basically it would have been a good film without: Neo, 5000 half naked hippies dancing in a cave, the French guy & his mrs, the entire ending after neo steps through the door.