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The answers to some of these questions may be implicit in the computer mechanics that the Matrix represents: A fight could be two cyber-entities--a software module and the neural impulses of a jacked-in human--"punching" to infect each other's code and "parrying" by mutating into immunity from that punch. The end of the first film suggested that Neo's power stems from his newfound ability to see the code, i.e., bits and bytes, behind the Matrix's "reality" and to therefore respond to what's really there rather than to the image.
But can anybody keep all this stuff in his or her head in a useful way while watching the film?
The last few scenes include a baffling event that points toward a possible upcoming explanation in part three. We won't spoil it, but, if it's where we're heading--and it could be a total red herring--things could turn out to be either very satisfying or very irritating. Be forewarned that Matrix Reloaded really is only half of a two-part story. Unlike The Matrix, it ends with a cliffhanger and represents less of an independent whole. (If you sit through the nine or so minutes of closing credits, you'll see a preview of The Matrix Revolutions.)
In the meanwhile, for all these problems big and little, the Wachowskis still hold the current franchise on intellectually engaging action films. It's not like I won't be heading back for a second (or even third) look.