Both use the same underlying technology (XMPP) and both know how to use the protocol, but it's still very hard to pull off at this scale once you allow multiple devices to login with the same account.
Skype just has vastly more features, that's why they have these synchronisation issues.
Since when does Skype use XMPP? AFAIK, it uses a closed protocol. It appears that Whatsapp does indeed use XMPP under the hood, though.
As for Skype, it's absolutely terrible at handling multiple devices. It would get much better if the app phoned home when a given message arrived on a Skype client with a focused window, in order to prevent/cancel already existing alerts on other devices.
With MS' Lync at work, if I forget to signout on my phone, a few times a day, my phone grabs an inbound message that never shows up on my desktop, and I totally miss the conversation. Skype has a lot of similar issues, and it's painful at best.
What I REALLY want is something for the workplace to kill Lync...
Just one example....when the connection is bad, it degrades audio and video, so neither is usable. And we won't even start on the nightmare that's the UI.
That MS paid a king's ransom for this and has done nothing with it since boggles the mind.
Microsoft also has a product called 'Lync' that (from what I've heard) is not doing so well, so I believe their goal there again is to roll their users into Skype and eventually discontinue that product. Buying Skype was all about trying to salvage their brand from the shortcomings of their own software.
It's doing pretty well in its market (Enterprise) because despite the demands (federation requires two servers) it's better than the competition (WebEx).
The client is slightly less annoying than Skype if only for the fact that it doesn't take over your entire computer for IM like the new Skype client does.
1) the mac client is buggy/crashy and sucks.
2) the mac client doesn't properly register itself so meeting links in outlook work.
3) when you are signed in on multiple systems, phone, home, work, messages aren't synchronized like gtalk/hangouts so you will miss a lot of conversations if you forget to sign out, this happens with my phone a couple times a week.
4) on a retina mac, the screen sharing only works on 1/4 the screen.
5) the UI in the android app is about the worst I've used for a productivity app on android.
On windows it's a bit better, but the non-synchronized conversations really irks me to no end.
Exactly! What do you have Skype installed on your smartphone?
A year from now on you might be saying: "Hey John Doe, I WhatsApped with my SO yesterday and asked her/him can I buy him/her some nice undies. You know what, today Facebook business pages are posting underwear ads on my wall!"
... or because skype clients start to "sync" with old chats when a different device comes online.