If people would read the directions, you would know to use your .me account as your iCloud login. If you had a .mac email, which I did, that should have been changed to .me years ago. Then, use your Apple iTunes store account Apple ID under Store.
For most people, this solves most problems.
The biggest problem is that many impulsively go ahead and enter into iCloud the Apple ID they use the most, the one from the App store.
Since I had a MobileMe account, and didn't want to screw things up, I carefully read the instructions from Apple.
That said, it would be nice if Apple would allow merging of Apple IDs. I don't understand why there is now a 90 day hold on using an Apple ID on an IOS device (I actually have a new one for the Apple Italy store, since I'm moving to Italy next year).