You should use separate Apple ID's for iCloud, iMessage and FaceTime. These services are separate from iTunes.
Create a new Apple ID > https://appleid.apple.com/cgi-bin/WebObjects/MyAppleId.woa/ -- Note: You need a verified email address
On one of the devices go:
Settings > iCloud > (Scroll Down) Delete Account > Sign in with the new Apple ID -- Note: This only affects the device
Settings > Messages > Send and Received > Apple ID > Sign Out > Sign in with the new Apple ID
Settings > FaceTime > Apple ID > Sign Out > Sign in with the new Apple ID
This will separate your iCloud content (i.e. Contacts, Notes, Reminders etc.), Messages and FaceTime.
You both can continue to use the same Apple ID for iTunes and share purchased Apps, Music and Movies