You are comparing Skype to WhatsApp? Don't you think it's kind of apples and oranges? Skype had technology that Facebook itself uses for video chat and WhatsApp supposedly has a large user base which mysteriously enough is so different than FB user base, that it's worth $16b?
As someone who is a heavy user of both Whatsapp, GTalk/Hangouts and FB Messenger, I find Whatsapp to be much faster than others. So, there could be some technological value to this deal.
Microsoft had its own Live Messenger and Lync too, so the acquisition in both cases was for the user base and the brand than technology IMO.