Using Skype on Windows Phone and Surface (as well on my desktop pc) it's now obvious to me that Skype contacts need to be merged with my Messenger contacts.
The duplication on a functional and visual standpoint is just messy and confusing. At least copy the Windows concept of linking if you're not able to integrate contacts.
The log-in for Skype is unintuitive. Maybe it's time to do away with the Skype log in and sensibly switch everything to Microsoft Account log in.
I find the Facebook log in pointless and seems to me just pandering to Facebook. Which is just bizarre. By adding another complication, it's diluting the message or concept of having one account across all services.
Please absorb Skype accounts with MS accounts and scrap the pointless and confusing Facebook log in.