Philip Seymour Hoffman was the better villain. I thought the 'captive hero' scenes in both films were incredible. MI3's story served the action as opposed to CR where the action served the story. MI3 had a decent story and perhaps fewer glaring issues than CR, but honestly it's just not really memorable.
I also feel the prequel elements got in the way of the story rather than helping it. Casino has a stronger overall story, even though I felt the lovey dovey stuff leading to the ending was just horrid and done completely wrong (in an Episode II 'sand is rough' sort of way). I give the overall nod to Casino Royale, although it falls apart at the end.
