In the third movie, we can see that The Oracle looks completely different. Obviously, this is because the original actor died, but the Wachowski's worked that into the plot. Unfortunately, I haven't quite figured out what that plot is.
Obviously, The Merovingian is responsible for this act. I did some more Googling on the topic and came across a small transcript from the Enter the Matrix video game that indicated the destruction codes were traded to The Merovingian by Rama Kandra. Rama Kandra got to keep his daughter safe and The Oracle got Sati whom she believes is very important to the future of both The Machine and Humans. But this doesn't explain why The Merovingian wanted to hurt The Oracle in the first place. Some people have suggested that it's because she helped Neo and the others steal The Keymaker, but this makes no sense as the code was traded before The Keymaker was stolen.
Another thing that makes no sense is The Oracle's indication that the reason she lost her shell is because she made a choice to help Neo and the others. What choice did she make? It can't have anything to do with The Keymaker for the reasons I specified above. Is this a case of contradictory canon or is there a solid explanation?