As of Skype for Business 2015, it's still SIP - S4B is more of a marketing maneuver than a real technical change. On the server side, applications built to integrate with Lync 2013 work seamlessly with S4B. The S4B client is just a reskin of the Lync 2013 client - it's a minor-minor revision number change, and still calls itself Lync 2013 on its About dialog.
Consumer Skype is still, to my knowledge, what it has always been.
However, Lync has been rebranded as Skype for Business. It's still Lync, and uses all of the same SIP-based protocols that it always has, since it was called Office Communicator.
I still haven't quite figured how they are going to mash the two together, or if they actually are going to. It is confusing having two completely different Skype clients on your desktop.
Now it's Skype and Skype for Business. S4B is a steaming heap compared to Skype in terms of features, and I think in the end consumers are going to end up confused and angry about this new Skype that doesn't have the features of the old one.
[1] https://technet.microsoft.com/en-us/library/gg398095.aspx
I have major problems with Lync/S4B's IM implementation. The most obvious are the lack of store-and-forward for messages to offline users and the poor to nonexistent support for persistent chat rooms (my solution: a "conference call" that's been going for weeks without anyone having turned on the audio). It's also very bad at handling changes in network connectivity, docking/undocking my laptop drops me from IM for at least a couple of minutes and often requires a restart of S4B.
I will agree that the softphone support is pretty good, but it's non-interoperable with our VoIP environment so it goes almost entirely unused. Unfortunately this has been the case everywhere I've worked except for one place that had WebEx and Cisco phones - those would get along with each-other sometimes if you were lucky, but it wasn't very reliable.
My point is that I've found the office communications landscape to be a terrible backwater of technology. I dislike Slack but I can see why it's taking off - most of the on-prem options for IM fail at basic IM features while adding VoIP/telepresence options that are non-interoperable and complex to implement and support. It says something that my employer has multiple FTEs dedicated to scheduling and setting up the videoteleconference rooms, because it takes a specialist just to make a call these days.
There are persistent chat rooms available (at least on-premise, if you install the extra server for them - not on Office365, though), but it's a little half-baked.
If we're piling on, there are some other kind of crummy limits, for a large enterprise IM platform. Sending an IM to a large number of recipients is pretty gimped (I believe the limit is in the 100-250 user range), because any chat between three or more users is bumped up into an AV conference. There's limitations on the number both of users who you can subscribe to presence updates, and how many other users can subscribe to your presence.
The client also seems to have some bad memory leaks. Particularly with any kind of extension that makes use of the COM API.