Hey! This is a really cool idea. The Matrix universe has a lot of unique themes that set it apart from most game systems, and even other cyberpunk settings. Could you give us a better idea of what your design goals for this are? That will make it a lot easier to evaluate rules you are writing, and determine whether they get you closer to your goals.
For example, what moments from the movies would you like to be possible in your system, that can't be done currently in D&D?