The Verge is reporting that Skype will indeed be built into the final version of Windows 8.1. This was expected as the messaging app had been neglected since its release in 8.0, and it was not included in the Windows 8.1 preview. Skype support will be built into the lock screen, as was demoed in the keynote yesterday, and you will be able to receive voice and video calls without logging in.
Microsoft bought Skype for $8.5 billion over two years ago. Back in April Microsoft forced Live Messenger users to start to migrate over to Skype.
Source: The Verge