I know this maybe quite off topic but I was asked to put in my two cents by Ushgarak, and I have no idea if this is the correct thread hehe.
I've already run a similar game to this on a different site (which went inactive quite a while ago now) and our main storyline was based around the second movie running into the third however we never included cannon characters unless completely necessary.
I have no problem with others playing cannons but more often than I'd like to see; there's ultimo-fans of the show out there that wanna play their fav character and do a poor job of it.
Now...as for the story line, I have no problem with playing alongside and sometimes slipping into the story of the Matrix movies but it'd be kinda cool and original if we just came up with something exactly that...original.