This post comes very late in the piece for good reason. I've only just seen the anime classic Ghost In The Shell (1998) for the first time in it's entirety. I recommend everyone to see it if you haven't already. The parallels between the Matrix storyline are a little too similar. From the code streams to the physical similarity between Major Kusunagi and Trinity/Neo, it seems that the Matrix 'plot' borrowed from GITS in a very major way.

That's not to say that I haven't enjoyed the Matrix/Matrix Reloaded films. I have - they're both visually exciting. Being a huge comic fan I've loved the storyboard look and the color contrasts and the general feel of the films. Personally I don't feel that any talk of valid plot lines should go by without mentioning Ghost. :)