Really? I thought the first one tied up pretty well. He defeated the agents when he jumped into them and did the Syfy channel flourescent light thing.
It told a complete arc, which aside from The Lord of the Rings/The Hobbit, every good first film has done in every series. The second film is the film where this isn't exactly required since its usually the fall of the hero.
The Machines weren't defeated though and humans were still in the Matrix against their will. Until all the humans that wanted to be out of the Matrix were out and there was at least some peace between them and the machines, then the story wasn't exactly over.