In Lync Server 2013 we can now federate with Skype, but in todays announcement it also says: The new Office comes with Skype. When you subscribe (To Office via Office 365), you get 60 minutes of Skype world minutes every month. Integrate Skype contacts into Lync and call or instant message anyone on Skype.
I also found this: Coming soon, with the full release of Office 365 Home Premium:
Talk to anyone using Skype, including 60 minutes of free international calls every month to landlines in over 40 countries and to cell phones in 7 countries. (Skype account required. Excludes special, premium and non-geographic numbers.)
So it will be intresting to see where this is going. and how these two services will fit. But from what i can tell, MS will push Skype to home users and Lync to Enterprise users. Kind of the same way as it is today so this feels natural.