My two cents on the Matrix -
Ok, they should have just stoppped at the first Matrix movie. I'm a huge Matrix fan, but that's only for the first movie. I'm not even buying the DVDs for the other two. Personally, Relvalotions and Reloaded rank with the Star Wars prequel triliogies for me. The first Matrix was an awesome movie, one of my all-time favs like LotR and Star Wars, the story was very interesting and creative. Yet, I really don't understand how people found the story confusing. And the continuation of the story with Reloaded and Revalotions.... the story was just filled with redunant and silly stuff.
I agree with BobtheDuck, MGS 2, had better plot twists and messed with you. Though, I wasn't really confused at-all by the story, I just found it strange.