Great question! I'll have to think on this some more, but:
1. I like Will's idea of recasting Matrix, but can't say I agree with his choices. McAvoy is great, but I'm still trying (in my mind) to dress him in shiny black neoprene.
I'd seriously consider Chiwetel Ejiofor (Talk To Me, Inside Man, Children of Men, American Gangster, Kinky Boots) as Trinity.
2. LOR: Daniel Day-Lewis as Aragorn? No way, just can't see it. First of all, too skinny for the warrior type role, although he played a good frontiersman in Last of the Mohicans. I just can't think of anyone else for this part -- Viggo did OK.
Instead of Fiennes as Boromir, I would now cast Daniel Craig in this role (with lifts in his boots, of course). Sean Bean was already typecast as the "bad" guy and the role of Boromir needed someone without a known quality. Boromir deserved better treatment (in books and film).
I'd not like to see Catherine Zeta-Jones in anything, thank you. Anne Hathaway has the right look...