The problem is not email, MobileMe. Or iCloud.
It is iTunes.
When Apple started iTunes Music Store before .Mac, MobileMe, and iCloud, all you needed was a unique Apple ID for iTunes only, with any linked email address. The latter of which was alterable, but for licesning reasons your Apple ID was not.
Then came the online .Mac and MobileMe, now iCloud services. And, most importantly, the App Store, which, for iOS devices, is managed through iTunes.
The online services always used an email name as the Apple ID. This forced all online customers plust ITMS customers to have two Apple ID's.
When iOS came out this created a sync problem, inlcuding for licensed content. iOS and now iCloud require ONLY an email Apple ID. But iTunes does not.
So people can still have two Apple ID's for iTunes (including apps...very important because they and the new music streaming are where iCloud and iTunes intersect), but only ONE functions for syncing with iCloud.
Which one?
The one with the email Apple ID.
To get around this Apple requires everyone to use a NON-Apple email to 'verify" your old Apple ID, the one without the email. And then you must manually authorize that account on all your devices. The failure to do one properly acorss all apps and any application on a Mac or Windows system will create either/or orphan/duplicate data. Worse, as people are finding out on Apple TV's, it will not allow for some iTunes purchases to show.
Because of this issue, Aplpe is not allowing:
1) Merging accounts. Apparently there are licensing and technical issues here. This would solve the problem outright as many have guessed astutely, but for some reason Apple is not prepared to go down this path.
2) Use of your .me or .mac email addresses to veify your original (non-email) Apple ID. This is causing by far the most problems as many people only use a single Apple-generated email. Worse, for many, their original Apple ID is inextricably linked to an ancient email account, no longer functioning, that pre-dates even .Mac, and goes to the originas of ITMS.
So the problem is with Apple because they force created two Apple ID's originally distinct (ITMS, then .Mac, MobileMe, iCloud), but are now forced to sync all of these ID's without allowing them to merge.
What to do? Keep complaining and taking up Genius tme and the phone and service chats. Email Tim Cook. Tell the media. Submit feedback. Dispute purchases.
It's a mess. It's Apple's mess. It needs fixing.