There is one main reason for Skype's terrible call quality these last years, and that is because it's no longer peer to peer as it was at it's beginning. All Skype calls go through Microsoft's servers, as far as I understand. I expect WhatsApp can make use of P2P (I suppose WebRTC) as I also find the phone calls excellent quality and have come to use it a lot. I'll definitely be ditching Skype very soon once video is proven.
Most cellular networks run behind symmetric carrier grade NATs. Even when you have two mobile devices behind the same NAT their traffic will not flow P2P. All traffic has to be routed to the public net (and then back in if you can figure out IP:Port which is usually not possible with symmetric NATs). They will never be hair-pinned on the NAT either... True P2P is only possible when at least one mobile device is on a public network or behind a more permissive NAT device.
I think @telesilla's point is that a Skype call would be going through all the cellular network's infrastructure, and then off to Microsoft, before coming back.
It's an extra link in the chain, meaning another potential bottleneck and added latency.
