Here is the solution: "backup both devises in iTunes FIRST on your computer, just in case."
1. Use your Apple ID for iTunes only or for iTunes and your iPhone.
2. Under settings: "Store" make sure the iTunes ID is in place, she will still have access to everything in your iTunes account, "Apps, music, movie, etc.".
3. Create a new iCloud account for your wife's iPhone FIRST, on the devise or a computer. This you will do under the "Mail, Calendar, etc" in settings. There you can turn on all that you want sync'd to iCloud.
4. Now you can goto "Settings–iCloud" and delete or change which iCloud account will be the main one on that devise.
5. On your devise, goto "Settings–iCloud–Storage & backup–Manage Storage" and delete your wife's information backup. This should remove her information from your devise. If not you can delete her information from your phone and your information from her phone.
Remember you have as many mail accounts as you need. If you two want to share a calendar then use the same iTunes ID or create a one just for sharing information you want shared.
Let me know if this helps.
I have 2 iPhones, one for myself, one for my wife. We shared the same Apple ID. Everything worked great, but now ...
Now, with iCloud, our contacts, bookmarks, appointments, etc., are merged - now what we want. I assume the answer if for her to have her own Apple ID. But the question is, what about all the apps she purchased using my Apple ID ... which she have to repurchase them?
Any other solutions?